Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Histone deacetylase 4 reverses cellular senescence via DDIT4 in dermal fibroblasts

ABSTRACT: Histone deacetylases (HDACs) are known to be a class of enzymes that remove acetyl groups from lysine chains on histones or other proteins, and play a crucial role in epigenetic regulation and aging process. Previous studies have identified that HDAC4 is down-regulated in aged and UV-irradiated skin in vivo. Therefore, HDAC4 may be an important role in skin aging process. However, the role of HDAC4 in skin aging is rarely known. In this study, we conducted the integrative transcriptome analysis of overexpression and knockdown of HDAC4, and UV- or H2O2-induced senescence in human dermal fibroblast and identified candidate genes which are regulated by HDAC4. Among these genes, DNA damage-inducible transcript 4 (DDIT4) was significantly regulated by HDAC4. We demonstrated that DDIT4 expression was downregulated during senescence and HDAC4 overexpression prevented senescence-induced decrease of DDIT4. In addition, overexpression of DDIT4 reduced SASP and aged-related genes that could promote aging, suggesting that DDIT4 may prevent senescence. Collectively, our results have shown that HDAC4 may play an important role in preventing skin aging by inducing DDIT4 expression.

ORGANISM(S): Homo sapiens

PROVIDER: GSE181329 | GEO | 2021/12/31

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Shared Molecules

Only show the datasets with similarity scores above: 0.5

Threshold

0.5

Similar Datasets

ANT2 accelerates cutaneous wound healing in aged skin by reverse senescence

Project description:An effective healing response is critical to healthy aging. Thus, the connection of regeneration and aging is needed to understand the complicated age-related healing process. Energy metabolism has been a common hallmark of both studies. In recent years, it become an emerging factor of skin homeostasis. Adenine nucleotide translocase-2 (ANT2) is a known cell proliferation marker and mediator of ATP import into mitochondria for energy homeostasis. Although energy homeostasis and the maintenance of mitochondrial function are critical for wound healing, the role of ANT2 in wound healing has not been elucidated. We found that ANT2 expression decreased during aging in mouse skin as well as during cellular senescence. Interestingly, overexpression of ANT2 in aged mouse skin promoted the healing of full-thickness cutaneous wounds. In addition, upregulation of ANT2 in replicative senescent human diploid dermal fibroblasts (HDFs) induced cell proliferation and migration, which are critical for the wound healing process. Furthermore, overexpression of ANT2 increased ATP production rate by activating the glycolysis pathway and also increased mitophagy, both of which are involved in energy homeostasis. Notably, ANT2-mediated upregulation of HSPA6 in aged HDFs inhibited the expression of pro-inflammatory genes that mediate cellular senescence and mitochondrial damage. This study demonstrates a new physiological role of ANT2 in skin wound healing via regulation of cell proliferation, energy homeostasis, and inflammation. Thus, our study links energy metabolism to skin homeostasis and identifies a genetic factor for improving wound healing with aging model.

2022-11-21 | GSE206141 | GEO

An Improved Human 3D Skin Model for Aging Research

Project description:Current models used to study skin aging, including in vivo murine models, ex vivo human skin, and in vitro 2D cell cultures, present significant limitations in replicating the complexity of chronological human skin aging. To address this gap, we developed a novel 3D human full-thickness skin aging model using primary dermal fibroblasts and epidermal keratinocytes harvested from the same aged donors (average age 80 years). Comprehensive histological, immunostaining, and transcriptomic analyses of this aging model, compared to a young 3D skin model (average age 20 years), revealed distinct hallmarks of chronological skin aging, including reduced epidermal and dermal thickness, decreased extracellular matrix content, diminished cell proliferation, and increased cellular senescence. Furthermore, 3D aging skin model also showed reduced IGF-1 expression and induction of AP1/JunB, which were consistent with observations in aged human skin. Transcriptomic profiling further identified upregulated pathways associated with extracellular matrix degradation, cellular senescence, and immune responses, aligning closely with published data from human aged skin. This novel in vitro model faithfully recapitulates several key features of chronological skin aging, offering a robust platform for studying aging mechanisms and testing therapeutic interventions. We have used microarray to study the gene expression profile of 3D skin models

2025-03-31 | GSE292398 | GEO

Downregulation of miR-15b is associated with increased SIRT4 expression in premature senescence and photoaging of the skin

Project description:Sirtuins are deacetylases or ADP-ribosyltransferases which are implicated in multiple pathways involved in metabolism and life-span regulation. Here, we link the mitochondrial sirtuin SIRT4, which overexpression negatively impacts on mitochondrial oxidative capacity, with premature senescence and skin aging. Accordingly, SIRT4 mRNA levels were significantly increased in vitro in human dermal fibroblasts after repetitive UVB exposure or in senescence triggered by mitotic spindle stress or ionizing radiation. Similarly, analysis of SIRT4 expression in vivo in human skin revealed upregulation of SIRT4 mRNA levels in the dermal compartment of photaged skin as compared with the dermis of intrinsically aged skin. In all our in vitro models, upregulation of SIRT4 expression was associated with decreased levels of miR-15b. Also, in human skin, highest copy numbers of miR-15b mRNA were detected in the epidermis, and epidermal expression was significantly reduced in photoaged skin as compared with intrinsically aged skin. Reduced miR-15b expression is most likely causally linked to increased SIRT4 expression because we found that (i) miR-15b displays a conserved and direct binding site within the 3'-untranslated region of the SIRT4 gene as demonstrated by luciferase reporter assays and (ii) transfection of oligonucleotides mimicking miR-15b function was sufficient to prevent SIRT4 upregulation in senescent cells in vitro. Thus, we propose that miR-15b acts as a negative regulator of SIRT4 expression to antagonize mitochondrial dysfunction and hence cellular senescence as well as tissue aging, in particular photoaging of the skin.

2016-06-08 | GSE45729 | GEO

Stabilizing Heterochromatin by DGCR8 Alleviates Senescence and Osteoarthritis

Project description:DiGeorge syndrome critical region 8 (DGCR8) is a critical component of the canonical microprocessor complex for microRNA biogenesis. However, the non-canonical functions of DGCR8 have not been studied. Here, we demonstrate that DGCR8 plays an important role in maintaining heterochromatin organization and attenuating aging. An N-terminal-truncated version of DGCR8 (DR8dex2) accelerated senescence in human mesenchymal stem cells (hMSCs) independent of its miRNA-processing activity, which is mediated by its C-terminal domains. Further studies revealed that DGCR8 maintained heterochromatin organization by interacting with the nuclear envelope protein Lamin B1, and heterochromatin-associated proteins, KAP1 and HP1 Overexpression of any of these proteins, including DGCR8, reversed premature senescent phenotypes in DR8dex2 hMSCs. Finally, DGCR8 was downregulated in pathologically and naturally aged hMSCs, whereas DGCR8 overexpression alleviated hMSC aging and osteoarthritis in mice. Taken together, these analyses uncovered a novel, miRNA processing-independent role for DGCR8 in maintaining heterochromatin organization and attenuating senescence. DGCR8 may therefore represent a new therapeutic target for alleviating human aging-related disorders.

2019-05-28 | PXD013856 | Pride

HDAC4 interactors identified by MS/MS

Project description:Access to DNA is the first level of control in regulating gene transcription, a control that is also critical for maintaining DNA integrity. Cellular senescence is characterized by profound transcriptional rearrangements and accumulation of DNA lesions. Here, we discovered an epigenetic complex between HDAC4 and HDAC1/HDAC2 that is involved in the erase of H2BK120 acetylation. The HDAC4/HDAC1/HDAC2 complex modulates the efficiency of DNA repair by homologous recombination, through dynamic deacetylation of H2BK120. Deficiency of HDAC4 leads to accumulation of H2BK120ac, impaired recruitment of BRCA1 and CtIP to the site of lesions, accumulation of damaged DNA and senescence. In senescent cells this complex is disassembled because of increased proteasomal degradation of HDAC4. Forced expression of HDAC4 during RAS-induced senescence reduces the genomic spread of γH2AX and affects H2BK120ac levels, which are increased in DNA-damaged regions accumulated during RAS-induced senescence. In summary, degradation of HDAC4 during senescence causes the accumulation of damaged DNA and contributes to the activation of the transcriptional program controlled by super-enhancers that maintains senescence.

2024-10-17 | PXD051316 | Pride

The comparison of MicroRNA profile of the dermis between young and old human

Project description:Skin aging is a process of structural and compositional remolding that can be manifested as wrinkling and sagging. Remarkably, the dermis plays a dominant role in the process of skin aging. Recent studies suggest that microRNAs (miRNAs) may play a role in the regulation of gene expression in organism aging. However, studies about age-related miRNAs in human skin remain limited. In order to obtain an overall view of miRNAs expression in human aged dermis, we have investigated the alteration of microRNAs during aging by examining biopsies of human dermis from 12 young and aged donors, and demonstrated that numerous microRNAs showed significant alteration in dermis tissue. Normal human dermal tissue from 12 consenting individuals. Old group vs young group. Old group: with the age over 60 years old; young group: with the age below 10 years old; each group was constituted of 6 individuals.

2016-02-05 | E-GEOD-72264 | biostudies-arrayexpress

Effect of rice fermentation and succinic acid on gene expression of human dermal fibroblasts irradiated with UVA

Project description:Skin aging caused by UV is called photoaging, which is characterized by deeper wrinkles accompanied by senescence of dermal fibroblasts and reduction of collagens. Rice fermentation, widely used in the cosmetics, has been reported to possess anti-aging benefits on skincare, however, its roles in the skin photoaging remains unclear. In this study, the effects of Maifuyin (a rice fermentation), and its ingredients succinic acid (SA) and choline on UVA-induced senescence in fibroblasts were evaluated. A mRNA sequencing technology (RNA-seq) was applied to study the effects of these ingredients on UVA-induced photoaging. In conclusion, these results highlight the potential use of Maifuyin and SA as promising agents for anti-photoaging applications.

2023-08-10 | GSE240226 | GEO

Molecular Rejuvenation of Gene Expression Pattern of Photoaged and Intrinsically Aged Human Skin by Broadband Light Treatment

Project description:Studies in model organisms suggest that aged cells can be functionally rejuvenated, but whether this concept applies to human skin is unclear. Here we apply deep sequencing of RNA 3' ends ("3-seq") to discover the gene expression program associated with human photoaging and intrinsic skin aging (collectively termed "skin aging") and the impact of broadband light (BBL) treatment. We find that skin aging was associated with the significantly altered expression level of 2,265 coding and noncoding RNAs, of which 1,293 became "rejuvenated" after BBL treatment, i.e. more similar in expression level of youthful skin. Rejuvenated genes (RGs) included several known key regulators of organismal longevity and their proximal long non-coding RNAs. Skin aging is not associated with systematic changes in 3' end mRNA processing. Hence, BBL treatment can restore the gene expression pattern of photoaged and intrinsically aged human skin to resemble young skin. In addition, our data reveals a novel set of targets that may lead to new insights into the human skin aging process. Examination of broadband light treated and untreated human skin transcriptomes of 5 women aged 50 years or more. They were compared to the skin transcriptomes of 5 young women aged 30 years or less.

2012-07-30 | E-GEOD-39170 | biostudies-arrayexpress

Unveiling a Novel in-vitro Model of Skin Inflamm-Aging: Validation of Terminalia chebula Extract and Supermolecular Bakuchiol for Reversal of Inflamm-Aging

Project description:Introduction: Sensitive skin is characterized by skin barrier disruption which is usually prone to react to external stimuli including UV, air pollution as well as cosmetic allergens. Sensitive skin tends to react with oxidative stress factors that could further lead to skin inflammation resulting in inflamm-aging. But almost no inflamm-aging models for sensitive skin, so it is worth constructing a method to screen anti-inflammaging ingredients and products. Methods: An in-vitro macrophages-fibroblasts model was established to evaluate the anti-inflammaging effect of ingredients. M1 phenotype and aging-associated gene expression were recorded by qPCR test to validate the inflamm-aging model. RNA sequencing was used to further elaborate the inflamm-aging mechanism of two validated ingredients. Results and conclusion: A novel in-vitro model of sensitive skin inflamm-aging was constructed by applying M1 phenotype of THP-1 culture medium supernatant to introduce the cellular senescence of the fibroblast cells, which could be used to screen out anti-inflammaging ingredients. In this model, supramolecular bakuchiol could promote collagen COL1A1 and COL3A3 production and inhibit inflammatory factors by increasing anti-inflammatory gene transcription (PTX3, ADAM33, and PDLIM1), while Terminalia chebula extract can inhibit cell senescence by reducing transcription of MAP4K2, and inflammatory factors CCL3 accumulation.

2025-04-16 | GSE286316 | GEO

UFMylation maintains YAP stability to promote vascular endothelial cell senescence

Project description:Endothelial cell senescence is an accomplice for vascular aging, which leads to cardiovascular diseases (CVD). Evidences showed that Hippo- Yes-associated protein (YAP) signaling pathway plays an essential role in aging-associated CVD. However, the exact role of YAP protein in endothelial cell senescence remains not fully clear. Here, we reported that YAP was elevated in senescent human umbilical vein endothelial cells (HUVECs) and inhibition of YAP by either specific siRNAs or inhibitor Verteporfin could attenuate HUVECs senescence. In contrast, overexpression of YAP induces cell senescence. Besides, we found that UFMylation activity and YAP were both elevated in senescent cells. Mechanistically, we found that UFMylation, a newly identified ubiquitin-like modification with essential biological functions, maintains the stability of YAP and further found that YAP is a substrate for UFMylation. Importantly, we found that compound 8.5, an inhibitor of E1 of UFMylation, can attenuate cell senescence with reduced YAP protein and alleviate vascular aging and improve cardiac function in aged mice. Therefore, compound 8.5 may be a potential small molecule for delaying vascular aging. Together, our finding provides molecular mechanism by which UFMylation maintains YAP stability and exerts an important role in promoting cell senescence, and identified that a previously unrecognized UFMylation is a potential therapeutic target for anti-aging.

2025-01-08 | GSE273828 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data