A multidimensional systems biology analysis of cellular senescence in aging and disease

Propagation of senescent phenotypes by extracellular HMGB1 is dependent on its redox state

BACKGROUND & PURPOSE

Cellular senescence spreads systemically through blood circulation, but its mechanisms remain unclear. High mobility group box 1 (HMGB1), a multifunctional senescence-associated secretory phenotype (SASP) factor, exists in various redox states. Here, we investigate the role of redox-sensitive HMGB1 (ReHMGB1) in driving paracrine and systemic senescence.

METHODS

We applied the paracrine senescence cultured model to evaluate the effect of ReHMGB1 on cellular senescence. Each redox state of HMGB1 was treated extracellularly to assess systemic senescence both in vitro and in vivo. Senescence was determined by SA-β-gal & EdU staining, p16INK4a and p21 expression, RT-qPCR, and Western blot methods. Bulk RNA sequencing was performed to investigate ReHMGB1-driven transcriptional changes and underlying pathways. Cytokine arrays characterized SASP profiles from ReHMGB1-treated cells. In vivo, young mice were administered ReHMGB1 systemically to induce senescence across multiple tissues. A muscle injury model in middle-aged mice was used to assess the therapeutic efficacy of HMGB1 blockade.

RESULTS

Extracellular ReHMGB1, but not its oxidized form, robustly induced senescence-like phenotypes across multiple cell types and tissues. Transcriptomic analysis revealed activation of RAGE-mediated JAK/STAT and NF-κB pathways, driving SASP expression and cell cycle arrest. Cytokine profiling confirmed paracrine senescence features induced by ReHMGB1. ReHMGB1 administration elevated senescence markers in vivo, while HMGB1 inhibition reduced senescence, attenuated systemic inflammation, and enhanced muscle regeneration.

CONCLUSION

ReHMGB1 is a redox-dependent pro-geronic factor driving systemic senescence. Targeting extracellular HMGB1 may offer therapeutic potential for preventing aging-related pathologies.

Molecular signatures of cellular senescence in cancer: a critical review of prognostic implications and therapeutic opportunities

Cellular senescence is a state of permanent loss of proliferative capacity. Therefore, cells that reach a senescent state prevent tumor initiation, acting as an anti-tumor mechanism. However, despite not being proliferative, senescent cells have high secretory activity, constituting the Senescence-Associated Secretory Phenotype (SASP). SASP includes thousands of soluble molecules and extracellular vesicles, through which senescent cells can affect other cells and the extracellular matrix. In advanced tumors, the enrichment of senescent cells can have anti- or pro-tumor effects depending on features like SASP composition, tumor microenvironment (TME) composition, the anatomic site, histopathologic characteristics of malignancy, and tumor molecular background. We reviewed the studies assessing the impact of the senescence status, measured by mRNA or lncRNA molecular signatures, in the prognosis and other clinically relevant information in cancer, including anti-tumor immunity and response to therapy. We discussed the pros and cons of different strategies to define those molecular signatures and the main limitations of the studies. Finally, we also raised clinical challenges regarding the crossroad between cellular senescence and cancer prognosis, including some therapeutic opportunities in the field.

Conserved biological processes in partial cellular reprogramming: Relevance to aging and rejuvenation

Partial or transient cellular reprogramming is defined by the limited induction of pluripotency factors without full dedifferentiation of cells to a pluripotent state. Comparing in vitro and in vivo mouse studies, and in vitro studies in humans, supported by visualizations of data interconnections, we show consistent patterns in how such reprogramming modulates key biological processes. Generally, partial reprogramming drives dynamic chromatin remodelling, involving histone modifications that regulate accessibility and facilitate pluripotency gene activation while silencing somatic identity. These changes are accompanied by modifications in stress response programs, such as inflammation, autophagy, and cellular senescence, as well as improved mitochondrial activity and dysregulation of extracellular matrix pathways. We also underscore the challenges in evaluating complex processes like aging and cellular senescence, given the variability in biomarkers used across studies. Overall, we highlight biological processes consistently influenced by reprogramming while noting that some effects are context-dependent, varying according to cell type, species, sex, recovery time, and the reprogramming method employed. These insights inform future research and potential therapeutic applications in aging and regenerative medicine.

Lnc-RAINY regulates genes involved in radiation susceptibility through DNA:DNA:RNA triplex-forming interactions and has tumor therapeutic potential in lung cancers

Lung cancer is the leading cause of cancer related deaths worldwide. Unfortunately, radiation resistance remains a major problem facing lung cancer patients. Recently, we identified a group of long non-coding RNAs (lncRNAs) known as linc-SPRY3 RNAs, expressed on the Y-chromosome, which play a role in radiation sensitivity by decreasing tumor burden in vitro and in vivo after radiation. In this study, we found that the linc-SPRY3 RNAs are one large lncRNA that we named Radiation Induced Y-chromosome linked long non-coding RNA (lnc-RAINY). Through ATAC-seq and immunoprecipitation experiments, we show that lnc-RAINY interacts with DNA in a triple helix to induce chromatin remodeling and gene expression. We also identified that lnc-RAINY regulates CDC6 and CDC25A expression affecting senescence induction, cell migration patterns, and cell cycle regulation. Furthermore, the administration of Lnc-RAINY encapsulated in FDA-approved nanoparticles into a lung cancer patient-derived xenograft model dramatically reduces tumor progression demonstrating therapeutic potential.

Associations of volatile organic compounds with accelerated epigenetic aging in the lungs of smokers and electronic cigarette users

BACKGROUND

Cigarette smoke and electronic cigarettes (EC) contain volatile organic compounds (VOCs) that can irritate the respiratory tract and affect pulmonary health. No studies have reported relationships between VOCs from smokers and EC users and pulmonary cellular behavior, such as lung biological aging.

METHODS

Using urinary total nicotine equivalent (TNE) and propylene glycol, the primarily E-liquid constituent, the tobacco use status of smokers (SM, n = 13), EC users (n = 12), and never-smokers (NS, n = 31) was confirmed. In the lungs of SM and EC, we assessed methylation age (mAge) estimates and cellular senescence-related gene expression. Ten urinary metabolites of VOCs with and without adjusting for nicotine intake, TNE, were associated with mAge estimates and gene expression.

RESULTS

Compared to EC users, SM had a significantly higher level of TNE-adjusted metabolites of acrylonitrile and 1,3-butadiene, while showing a lower level of a metabolite of benzene. TNE-adjusted metabolites of 1,3 butadiene, ethylene oxide, and acrylonitrile were overall positively associated with Pheno-mAge (an epigenetic clock for lifespan/mortality), with different patterns of the associations by smoking group. IFNG and STAT1 showed an overall positive association with TNE-adjusted metabolites of propylene oxide and acrylamide, with a stronger association in SM compared to EC. Without controlling for TNE, a benzene metabolite was the only significant associated with POU5F1.

CONCLUSIONS

This is the first study reporting associations between smoking/EC-related VOCs and lung biological aging with strong associations in SM, supporting the need for further research on the roles of VOCs-related epigenetic aging and cell senescence genes in pulmonary diseases.

Interspecific interactions and aging: Prediction of gerogenic bacteria and critical human protein targets of microbial infections

Bacteria permeate every niche of the human body with major consequences on our health and senescence that have not been fully described. Here, we predict which bacteria and which bacterial proteins could interfere with proteins associated with human aging using bipartite networks showing interspecific protein interactions coupled with investigations of published experimental evidence and transcriptomic data. We introduce the term of "gerogenic" bacteria, literally bacteria that could induce some aging in their host and discuss the mechanisms by which such bacteria could serve as age-distorters of humans. Salmonella, Escherichia and Shigella appear as major candidate age-distorters, characterized by a higher experimentally demonstrated potential than other bacteria to interact with human proteins associated with human aging and human cellular senescence. Our analysis also highlights an evolutionary convergence among bacterial and viral candidate age-distorting proteins, since 14 human proteins associated with aging can be commonly targeted by bacteria and viruses in case of microbial infection. Since infections are common and Salmonella, Escherichia and Shigella are frequently found as pathogens in our microbiomes, characterizing bacterial influence on our aging and our cellular senescence through molecular hijacking could enhance the understanding of the causes of aging and suggest new anti-aging therapies.

In vitro senescence and senolytic functional assays

A detailed understanding of aging biology and the development of anti-aging therapeutic strategies remain imperative yet inherently challenging due to the protracted nature of aging. Cellular senescence arises naturally through replicative exhaustion and is accelerated by clinical treatments or environmental stressors. The accumulation of senescent cells-defined by a loss of mitogenic potential, resistance to apoptosis, and acquisition of a pro-inflammatory secretory phenotype-has been implicated as a key driver of chronic disease, tissue degeneration, and organismal aging. Recent studies have highlighted the therapeutic promise of senolytic drugs, which selectively eliminate senescent cells. Compelling results from preclinical animal studies and ongoing clinical trials underscore this potential. However, the clinical translation of senolytics requires further pharmacological validation to refine selectivity, minimize toxicity, and determine optimal dosing. Equally important is the evaluation of senolytics' potential to restore tissue structure and function by reducing the senescent cell burden. In vitro tissue culture models offer a powerful platform to advance these efforts. This review summarizes the current landscape of in vitro systems used for inducing cellular senescence-referred to as "senescence assays"-and for screening senolytic drugs-referred to as "senolytic assays". We conclude by discussing key challenges to improving mechanistic insight, predictive accuracy, and clinical relevance in senolytic drug development, as well as emerging applications of senolytic therapies.

Tobacco smoking exposure-mediated ELAVL1 regulates bladder cancer cell senescence via autophagy activation

Tobacco smoking is a well-established risk factor for bladder cancer, which shows connection to cell senescence in various diseases. However, the regulatory mechanisms linking tobacco smoking exposure to senescence regulation in bladder cancer remain incompletely characterized. In this investigation, we demonstrated that the smoking carcinogen 4-aminobiphenyl (4-ABP) inhibited cell senescence while enhancing proliferative, invasive, and migratory capacities of bladder cancer cells, as evidenced by SA-β-gal staining, western blot and cell malignant phenotype experiments. We further identified 275 cell senescence-related genes specific to bladder cancer based on CellAge database, the Nanjing bladder cancer dataset and public database. Through genome-wide association studies in 580 bladder cancer cases and 1101 controls, we pinpointed that rs12978895 G>A in ELAVL1 was significantly correlated with decreased bladder cancer risk (odds ratio = 0.79, 95 % confidence interval = 0.68-0.92) and interacted with smoking (P = 0.043). In genetic regulation, both experimental and population study showed that the A allele of rs12978895 significantly reduced ELAVL1 expression, while elevated ELAVL1 levels were observed in tumor tissues. Notably, exposed to smoking carcinogen 4-ABP resulted in a markedly increased expression of ELAVL1, which inhibited senescence of bladder cancer cells. Mechanistically, 4-ABP upregulated ELAVL1 suppressed cell senescence through autophagy activation, thus promoting bladder cancer progression. This study elucidated the genetic susceptibility and biological function of ELAVL1 in tobacco smoking exposure cell models, shedding light on the etiology of bladder cancer.

Maximum lifespan and brain size in mammals are associated with gene family size expansion related to immune system functions

Mammals exhibit an unusual variation in their maximum lifespan potential, measured as the longest recorded longevity of any individual in a species. Evidence suggests that lifespan increases follow expansion in brain size relative to body mass. Here, we found significant gene family size expansions associated with maximum lifespan potential and relative brain size but not in gestation time, age of sexual maturity, and body mass in 46 mammalian species. Extended lifespan is associated with expanding gene families enriched in immune system functions. Our results suggest an association between gene duplication in immune-related gene families and the evolution of longer lifespans in mammals. These findings explore the genomic features linked with the evolution of lifespan in mammals and its association with life story and morphological traits.

Deletion of Nrf1α exacerbates oxidative stress-induced cellular senescence by disrupting cell homeostasis

Cellular senescence is recognized as a fundamental hallmark contributing to ageing and various age-related diseases, with oxidative stress playing a critical initiating role in their pathological processes. However, the anti-senescence potential of the antioxidant nuclear factor erythroid-derived 2-like 1 (Nrf1, encoded by Nfe2l1) remains elusive, despite accumulating evidence demonstrating its role as an indispensable redox-determining transcription factor for maintaining cellular homeostasis and organ integrity. This study reveals that deletion of Nrf1α significantly elevates senescence characteristics in Nrf1α-/--deficient cells, as evidenced by two distinct experimental models. These cells exhibit heightened activity of senescence-associated β-galactosidase and progressive senescence-associated secretory phenotype (SASP), accompanied by decreased cell vitality and intensified cell cycle arrest. Further investigation uncovers that this acceleration of oxidative stress-induced senescence results from increased disturbance in cellular homeostasis. The Nrf1α-/- deficiency leads to STAG2- and SMC3-dependent chromosomal stability disruption and autophagy dysfunction, albeit being accompanied by excessive accumulation of Nrf2 (encoded by Nfe2l2). The aberrantly hyperactive Nrf2 cannot effectively counteract the escalating disturbance of cellular homeostasis caused by Nrf1α-/-. This study provides evidence supporting Nrf1α's essential cytoprotective function against stress-induced cellular senescence, highlighting its indispensable contribution to maintaining robust cell homeostasis during the senescence pathophysiological process.

Inhibiting the Histone Demethylase Kdm4a Restrains Cardiac Fibrosis After Myocardial Infarction by Promoting Autophagy in Premature Senescent Fibroblasts

Premature senescent fibroblasts (PSFs) play an important role in regulating the fibrotic process after myocardial infarction (MI), but their effect on cardiac fibrosis remains unknown. Here, the investigation is aimed to determine whether PSFs contribute to cardiac fibrosis and the underlying mechanisms involved. It is observed that premature senescence of fibroblasts is strongly activated in the injured myocardium at 7 days after MI and identified that Kdm4a is located in PSFs by the analysis of scRNA-seq data and immunostaining staining. Moreover, fibroblast specific gain- and loss-of-function assays showed that Kdm4a promoted the premature senescence of fibroblasts and cardiac interstitial fibrosis, contributing to cardiac remodeling in the advanced stage after MI, without influencing early cardiac rupture. ChIP-seq and ChIP-PCR revealed that Kdm4a deficiency promoted autophagy in PSFs by reducing Trim44 expression through increased levels of the H3K9me3 modification in the Trim44 promoter region. Furthermore, a coculture system revealed that Kdm4a overexpression increased the accumulation of PSFs and the secretion of senescence-associated secretory phenotype (SASP) factors, subsequently inducing cardiac fibrosis, which could be reversed by Trim44 interference. Kdm4a induces the premature senescence of fibroblasts through Trim44-mediated autophagy and then facilitates interstitial fibrosis after MI, ultimately resulting in cardiac remodeling, but not affecting ventricular rupture.

Identification of markers for neurescence through transcriptomic profiling of postmortem human brains

Neuronal senescence (i.e., neurescent) is an important hallmark of aging and neurodegeneration, but it remains poorly characterized in the human brain due to the lack of reliable markers. This study aimed to identify neurescent markers based on single-nucleus transcriptome data from postmortem human prefrontal cortex. Using an eigengene approach, we integrated three gene panels: a) SenMayo, b) Canonical Senescence Pathway (CSP), and c) Senescence Initiating Pathway (SIP), to identify neurescent signatures. We found that paired markers outperform single markers; for instance, by combining CDKN2D and ETS2 in a decision tree, a high accuracy of 99% and perfect specificity (100%) were achieved in distinguishing neurescent. Differential expression analyses identified 324 genes that are overexpressed in neurescent. These genes showed significant associations with important neurodegeneration-related pathways including Alzheimer's disease, Parkinson's disease, and Huntington's disease. Interestingly, several of these overexpressed genes are linked to mitochondrial dysfunction and cytoskeletal dysregulation. These findings provide valuable insights into the complexities of neurescent, emphasizing the need for further exploration of histologically viable markers and validation in broader datasets.

Integrative Bioinformatic Analysis of Cellular Senescence Genes in Ovarian Cancer: Molecular Subtyping, Prognostic Risk Stratification, and Chemoresistance Prediction

Background: Ovarian cancer (OC) is a heterogeneous malignancy associated with a poor prognosis, necessitating robust biomarkers for risk stratification and therapy optimization. Cellular senescence-related genes (CSGs) are emerging as pivotal regulators of tumorigenesis and immune modulation, yet their prognostic and therapeutic implications in OC remain underexplored. Methods: We integrated RNA-sequencing data from TCGA-OV (n = 376), GTEx (n = 88), and GSE26712 (n = 185) to identify differentially expressed CSGs (DE-CSGs). Consensus clustering, Cox regression, LASSO-penalized modeling, and immune infiltration analyses were employed to define molecular subtypes, construct a prognostic risk score, and characterize tumor microenvironment (TME) dynamics. Drug sensitivity was evaluated using the Genomics of Drug Sensitivity in Cancer (GDSC)-derived chemotherapeutic response profiles. Results: Among 265 DE-CSGs, 31 were prognostic in OC, with frequent copy number variations (CNVs) in genes such as STAT1, FOXO1, and CCND1. Consensus clustering revealed two subtypes (C1/C2): C2 exhibited immune-rich TME, elevated checkpoint expression (PD-L1, CTLA4), and poorer survival. A 19-gene risk model stratified patients into high-/low-risk groups, validated in GSE26712 (AUC: 0.586-0.713). High-risk patients showed lower tumor mutation burden (TMB), immune dysfunction, and resistance to Docetaxel/Olaparib. Six hub genes (HMGB3, MITF, CKAP2, ME1, CTSD, STAT1) were independently predictive of survival. Conclusions: This study establishes CSGs as critical determinants of OC prognosis and immune evasion. The molecular subtypes and risk model provide actionable insights for personalized therapy, while identified therapeutic vulnerabilities highlight opportunities to overcome chemoresistance through senescence-targeted strategies.

Macrophage-derived CTSS drives the age-dependent disruption of the blood-CSF barrier

The choroid plexus (CP) serves as the primary source of cerebrospinal fluid (CSF). The blood-CSF barrier, composed of tight junctions among the epithelial cells in the CP, safeguards CSF from unrestricted exposure to bloodborne factors. This barrier is thus indispensable to brain homeostasis and is associated with age-related neural disorders. Nevertheless, its aging is poorly understood. Here, we report that cathepsin S (CTSS), a protease secreted from the CP macrophages, is upregulated in aged CP due to increased cell senescence. CTSS cleaves the essential tight junction component, claudin 1 (CLDN1), and, in turn, impairs the blood-CSF barrier. Notably, inhibiting CTSS or upregulating CLDN1 in aged CP rejuvenates the blood-CSF barrier and brain functions. Our findings uncover a vital interplay between immune and barrier cells that accelerates CP and brain aging, identify CTSS as a potential target to improve brain homeostasis in aged animals, and underscore the critical role of circulating proteinases in aging.

Investigating Aging-Related Endometrial Dysfunction Using Endometrial Organoids

Ageing of the endometrium is a critical factor that affects reproductive health, yet its intricate mechanisms remain poorly explored. In this study, we performed transcriptome profiling and experimental verification of endometrium and endometrial organoids from young and advanced age females, to elucidate the underlying mechanisms and to explore novel treatment strategies for endometrial ageing. First, we found that age-associated decline in endometrial functions including fibrosis and diminished receptivity, already exists in reproductive age. Subsequently, based on RNA-seq analysis, we identified several changes in molecular processes affected by age, including fibrosis, imbalanced inflammatory status including Th1 bias in secretory phase, cellular senescence and abnormal signalling transduction in key pathways, with all processes been further validated by molecular experiments. Finally, we uncovered for the first time that PI3K-AKT-FOXO1 signalling pathway is overactivated in ageing endometrium and is closely correlated with fibrosis and impaired receptivity characteristics of ageing endometrium. Blocking or activation of PI3K by LY294002 or 740Y-P could attenuate the effect of ageing or accelerate dysfunction of endometrial organoids. This discovery is expected to bring new breakthroughs for understanding the pathophysiological processes associated with endometrial ageing, as well as treatment strategies to improve reproductive outcomes in women of advanced reproductive age.

Comprehensive assessment of the significance of cellular senescence-associated genes in neuroblastoma

BACKGROUND

The clinical course of high-risk neuroblastoma patients remains suboptimal, and the dynamic and reversible nature of cellular senescence provides an opportunity to develop new therapies.

OBJECTIVE

This study aims to identify unique markers of cellular senescence in neuroblastoma and to explore their clinical significance.

METHODS

The impact of multiple genetic regulatory mechanisms on cellular senescence-associated genes (CSAGs) was first assessed. We identified cellular senescence-associated subtypes by hierarchical clustering and explored the intrinsic differences between subtypes. We screened key CSAGs based on PPI networks and clinical significance. Subsequently, we constructed the cellular senescence-related risk score (CSRS) by LASSO regression and stepwise Cox regression, and validated its performance and stability through multiple methods. Finally, we performed single-cell analysis and constructed the nomogram.

RESULTS

The expression of CSAGs was influenced by copy number variation and DNA methylation. We found that significant differences between cellular senescence-associated subtypes in immune infiltration and overall prognosis. AURKA, CDK4, TERT were key genes in the cellular senescence process. CSRS showed superior and robust predictive performance in several cohorts and could serve as an independent prognostic factor in neuroblastoma. The senescence signature was also meaningful at the single-cell level and the nomogram was shown to have high accuracy and high clinical benefit.

CONCLUSIONS

We comprehensively evaluated the significance of cellular senescence in neuroblastoma and concluded that it was significantly associated with immune characteristics and overall prognosis. Based on the expression levels of CSAGs, we developed the CSRS, which was a reliable tool to contribute to prognostic assessment and clinical decision making.

Mechanisms of mitochondrial reactive oxygen species action in bone mesenchymal cells

Mitochondrial (mt)ROS, insufficient NAD+, and cellular senescence all contribute to the decrease in bone formation with aging. ROS can cause senescence and decrease NAD+, but it remains unknown whether these mechanisms mediate the effects of ROS in vivo. Here, we generated mice lacking the mitochondrial antioxidant enzyme Sod2 in osteoblast lineage cells targeted by Osx1-Cre and showed that Sod2ΔOsx1 mice had low bone mass. Osteoblastic cells from these mice had impaired mitochondrial respiration and attenuated NAD+ levels. Administration of an NAD+ precursor improved mitochondrial function in vitro but failed to rescue the low bone mass of Sod2ΔOsx1 mice. Single-cell RNA-sequencing of bone mesenchymal cells indicated that ROS had no significant effects on markers of senescence but disrupted parathyroid hormone signaling, iron metabolism, and proteostasis. Our data supports the rationale that treatment combinations aimed at decreasing mtROS and senescent cells and increasing NAD+ should confer additive effects in delaying age-associated osteoporosis.

Young fibroblast-derived migrasomes alleviate keratinocyte senescence and enhance wound healing in aged skin

BACKGROUND

Alterations in intercellular communication driven by cellular senescence constitute an important factor in skin aging. Migrasome, a newly discovered vesicular organelle, efficiently participates in intercellular communication; however, the relationship between cellular senescence and migrasomes remains unreported.

OBJECTIVE

This study aims to explore the possible relationship between cellular senescence and migrasomes formation, and investigate the effects of young fibroblast-derived migrasomes on senescent keratinocytes and wound healing in aged skin.

RESULT

Single-cell RNA sequencing (scRNA-seq) data analysis revealed that fibroblasts exhibited the highest level of transcriptional variability during skin aging, and the degree of fibroblast senescence negatively correlated with the expression level of migrasome-associated markers. Further multiplex Immunohistochemistry (mIHC) results suggested that younger mouse skin contained more migrasomes than older mouse skin. Transmission electron microscopy (TEM) observations demonstrated abundant migrasomes in the skin from young individuals. In vitro experiments indicated that young fibroblasts produced significantly more migrasomes than senescent fibroblasts, as confirmed by wheat germ agglutinin (WGA) staining and scanning electron microscopy (SEM). Importantly, purified migrasomes from young fibroblasts were found to reduce the expression of senescence-associated markers in HaCaT cells. In vivo, using a wound healing model in naturally aged mice, we observed that migrasomes derived from young fibroblasts not only accelerated wound healing but also reduced senescence-associated marker expression in the skin.

CONCLUSION

Migrasomes formation ability reduced during skin aging progress, and young fibroblast-derived migrasomes rejuvenated senescent keratinocytes and promoted wound healing in aged skin. These findings offer new ideas for alleviating skin aging and enhancing wound healing in aged skin.

A Novel Butyrate Derivative, Zinc Dibutyroyllysinate, Blunts Microphthalmia-Associated Transcription Factor Expression and Up-Regulates Retinol and Differentiation Pathway mRNAs in a Full-Thickness Human Skin Model

Lysine, butyric acid, and zinc play important roles in skin homeostasis, which involves aging, inflammation, and prevention of skin barrier disruption. This bioactivity spectrum is not replicated by any one topical compound currently in use. Our purpose in this study was to characterize a novel compound, zinc dibutyroyllysinate (ZDL), consisting of zinc with lysine and butyric acid moieties. We used RNA-seq to evaluate its effect on gene expression in a full-thickness skin model. We show that lysine alone has minimal effects on gene expression, whereas ZDL had greater transcriptional bioactivity. The effects of ZDL included an increased expression of genes promoting epidermal differentiation and retinol metabolism, along with a decreased expression of microphthalmia-associated transcription factor (MITF) and other melanogenesis genes. These effects were not replicated by an alternative salt compound (i.e., calcium dibutyroyllysinate). ZDL additionally led to a dose-dependent increase in skin fibroblast extracellular matrix proteins, including collagen I, collagen IV, and prolidase. Loss of melanin secretion was also seen in ZDL-treated melanocytes. These results provide an initial characterization of ZDL as a novel topical agent. Our findings support a rationale for the development of ZDL as a skincare ingredient, with potential applications for diverse conditions, involving melanocyte hyperactivity, pigmentation, inflammation, or aging.

Procyanidin A1 from Peanut Skin Exerts Anti-Aging Effects and Attenuates Senescence via Antioxidative Stress and Autophagy Induction

The aging population is steadily increasing, with aging and age-related diseases serving as major risk factors for morbidity, mortality, and economic burden. Peanuts, known as the "longevity nut" in China, have been shown to offer various health benefits, with peanut skin extract (PSE) emerging as a key compound of interest. This study investigates the bioactive compound in PSE with anti-aging potential and explores its underlying mechanisms of action. Procyanidin A1 (PC A1) was isolated from PSE, guided by the K6001 yeast replicative lifespan model. PC A1 prolonged the replicative lifespan of yeast and the yeast-like chronological lifespan of PC12 cells. To further confirm its anti-aging effect, cellular senescence, a hallmark of aging, was assessed. In senescent cells induced by etoposide (Etop), PC A1 alleviated senescence by reducing ROS levels, decreasing the percentage of senescent cells, and restoring proliferative capacity. Transcriptomics analysis revealed that PC A1 induced apoptosis, reduced senescence-associated secretory phenotype (SASP) factors, and modulated the phosphatidylinositol 3-kinase (PI3K)/protein kinase B (Akt) signaling pathway. The antioxidative capacity of PC A1 was also evaluated, showing enhanced resistance to oxidative stress in PC12 cells by reducing reactive oxygen species (ROS) and malondialdehyde (MDA) levels and increasing superoxide dismutase (SOD) activity. Moreover, PC A1 induced autophagy, as evidenced by an increase in fluorescence-labeled autophagic compartments and confirmation via Western blot analysis of autophagy-related proteins. In addition, the treatment of an autophagy inhibitor abolished the antioxidative stress and senescence-alleviating effects of PC A1. These findings reveal that PC A1 extended lifespans and alleviated cellular senescence by enhancing oxidative stress resistance and inducing autophagy, positioning it as a promising candidate for further exploration as a geroprotective agent.

Senescent macrophages trigger a pro-inflammatory program and promote the progression of rheumatoid arthritis

This study explores the complex mechanisms between Rheumatoid Arthritis (RA) and cellular senescence, with a focus on the role of four key genes (MMP1, CCL7, CXCL1, HK3) identified through transcriptome analysis in the GEO database. These genes are closely related to IL-17 signalling and the pathogenesis of RA. In a macrophage senescence model induced by hydrogen peroxide (H2O2) and bleomycin (BLM), quantitative real-time PCR (qRT-PCR) and Western blot confirmed the significant upregulation of these genes and an increase in the secretion of the cytokine IL-17, which promotes an inflammatory environment for the polarization of macrophages to M1. When co-cultured with mouse synovial fibroblasts (MSF), MSF showed enhanced vitality and increased invasiveness, indicating a key role for these genes in the progression of RA. Additionally, HK3, less reported in RA, when its expression is knocking down, lactate secretion and lactylation modification at lysine 14 of histone H3 in macrophages were reduced, leading to a change in macrophage polarity. The study concludes that the altered polarity of senescent macrophages drives the proliferation and invasion of MSF, significantly promoting the development of RA and providing insights into the pathophysiology of RA.

Transcriptomic profile of RNA pseudouridine modification as a biomarker for cellular senescence associated with survival outcomes in colorectal cancer

BACKGROUND

Colorectal cancer (CRC) is considered as an age-related disease, and cellular senescence (CS) plays a crucial role in cancer development and progression. Previous studies have shown the role of epigenetic changes in aging and cancer development, but the role of RNA pseudouridine (Ψ) modification in aging and cancer remains to be explored.

RESULTS

Using bulk RNA sequencing, CRC cells with low Ψ writers expression levels have higher CS levels. We developed the Psi Score for assessing the transcriptomic profile of RNA Ψ modification regulation and found that the Psi Score correlates with CS. Furthermore, Psi-related senescence may be mediated by mTOR, TGF-β, TNF-α, and inflammatory response signaling pathways. Meanwhile, Psi Score could predict the anti-cancer treatment outcomes of anti-aging interventions and could be used to predict the response to immunotherapy.

CONCLUSIONS

Overall, these findings reveal that RNA Ψ modification connected aging and cancer and provided novel insights into biomarker-guided cancer regimens.

SenSkin™: a human skin-specific cellular senescence gene set

Cellular senescence gene sets have been leveraged to overcome the inadequate sensitivity or specificity of single markers. However, growing evidence of heterogeneity among tissues in senescent cell phenotypes and gene expression profiles has highlighted the need for tissue-specific gene sets. SenSkin™ was curated by an expert review of literature on cellular senescence in the skin and characterized with pathway analysis. To validate SenSkin™, it was evaluated for enrichment with chronological aging in a bulk RNA-sequencing (RNA-seq) dataset and a pseudobulk RNA-seq dataset. Further, changes to SenSkin™ in different skin cell types with photoaging were evaluated in two single-cell RNA-seq datasets. SenSkin™ predominantly included genes related to the senescence-associated secretory phenotype (SASP), which were associated with metabolism and multiple aspects of immune responses. SenSkin™ was more enriched in chronologically aged skin than other commonly used cellular senescence and aging gene sets. In scRNA-seq, SenSkin™ displayed significant upregulation due to photoaging in ten skin cell types. In conclusion, SenSkin™ is a human skin-specific senescence gene set validated in chronological aging and photoaging, which may be more effective at detecting senescent cells in the skin than non-tissue-specific gene sets.

Senescence-specific molecular subtypes stratify the hallmarks of the tumor microenvironment and guide precision medicine in bladder cancer

BACKGROUND

Bladder cancer (BLCA) is notably associated with advanced age, characterized by its high incidence and mortality among the elderly. Despite promising advancements in models that amalgamate molecular subtypes with treatment and prognostic outcomes, the considerable heterogeneity in BLCA poses challenges to their universal applicability. Consequently, there is an urgent need to develop a new molecular subtyping system focusing on a critical clinical feature of BLCA: senescence.

METHODS

Utilizing unsupervised clustering on the Cancer Genome Atlas Program (TCGA)-BLCA cohort, we crafted a senescence-associated molecular classification and precision quantification system (Senescore). This method underwent systematic validation against established molecular subtypes, treatment strategies, clinical outcomes, the immune tumor microenvironment (TME), relevance to immune checkpoints, and identification of potential therapeutic targets.

RESULTS

External validations were conducted using the Xiangya cohort, IMvigor210 cohort, and meta-cohort, with multiplex immunofluorescence confirming the correlation between Senescore, immune infiltration, and cellular senescence. Notably, patients categorized within higher Senescore group were predisposed to the basal subtype, showcased augmented immune infiltration, harbored elevated driver gene mutations, and exhibited increased senescence-associated secretory phenotype (SASP) factors expression in the transcriptome. Despite poorer prognoses, these patients revealed greater responsiveness to immunotherapy and neoadjuvant chemotherapy.

CONCLUSIONS

Our molecular subtyping and Senescore, informed by age-related clinical features, accurately depict age-associated biological traits and its clinical application potential in BLCA. Moreover, this personalized assessment framework is poised to identify senolysis targets unique to BLCA, furthering the integration of aging research into therapeutic strategies.

Senolytics restore hematopoietic stem cell function in sickle cell disease

Sickle Cell Disease (SCD) is a blood disorder affecting millions worldwide. Emerging evidence reveals that SCD pathophysiology increases risk of myeloid malignancies and hematopoietic stem cell (HSC) dysfunction, possibly due to pathological stress on bone marrow. To investigate this further, we interrogated mice and individuals with SCD and observed extended cell cycle times, oxidative stress, DNA damage, senescence, and dysregulation of molecular programs associated with these processes in bone marrow hematopoietic stem and progenitor cells (HSPCs). Human SCD HSPCs displayed poor hematopoietic potential ex vivo . SCD mice displayed a dramatic loss of transplantable bone marrow HSPCs, which was reversed upon treatment of SCD mice with the senolytic agent, ABT-263 (navitoclax). Thus, senolytics restore bone marrow function during SCD in mice and represent a novel strategy to improve bone marrow health in individuals with SCD and improve the safety of potentially curative gene therapies that utilize autologous HSPCs from individuals with SCD.

Investigating the aging-modulatory mechanism of Rasayana Churna, an Ayurvedic herbal formulation, using a computational approach

This study investigates the impact and mechanisms of Rasayana Churna, an Ayurvedic poly-herbal formulation, in treating aging-related disorders through text mining, network pharmacology, molecular docking simulation, Super-MMPBSA, and density functional theory. The text mining of Rasayana Churna highlighted the diverse therapeutic potential of Phyllanthus emblica, Tinospora cordifolia, and Tribulus terrestris in managing aging-related disorders through their antidiabetic, antioxidant, and anti-inflammatory properties. Using network pharmacology, 17 bioactive compounds and 137 corresponding potential targets of Rasayana Churna were identified and used to construct protein-protein interaction and hub gene networks. Key targets such as AKT1, BCL2, ESR1, and GSK3B were linked to aging-related pathways, with GO and KEGG enrichment analyses highlighting processes like apoptosis, oxidative stress response, and pathways like PI3K-Akt signaling. Molecular docking analysis identified 14 compounds with strong binding affinity toward the key aging target AKT1. Three bioactive compounds-Kaempferol, N-Caffeoyltyramine, and Multifidol glucoside-exhibited superior stability and binding interactions in MD simulations, confirmed by RMSD, RMSF, Rg, hydrogen bonding, SASA, PCA, and free energy landscape analysis. Super-MMPBSA (last 30 ns) calculation was performed to analyze dynamic behavior and protein-ligand stability, revealing significantly lower ΔG binding free energy values for the three hit compounds (- 177.871, - 164.855, - 199.649 kJ/mol, respectively) compared to the AKT1-reference complex (- 109.463 kJ/mol). DFT analysis revealed favorable electronic properties and kinetic stability for these compounds. Integrating traditional Ayurvedic knowledge with computational techniques suggests Rasayana Churna could prevent and manage aging-related conditions. However, further in vitro, in vivo, and clinical studies are needed to validate its aging-modulatory potential.

Emerging therapeutic frontiers in prostate health: Novel molecular targets and classical pathways in comparison with BPH and prostate cancer

Current therapeutic strategies for benign prostatic hyperplasia (BPH) and prostate cancer focus mainly on androgen receptors (AR) and 5-alpha reductase inhibition to suppress androgen-driven prostate growth. However, these methods often result in side effects and resistance. Recent research identifies novel targets like integrin and cadherin inhibitors, gene regulation, microRNAs, cellular senescence, and metabolomics pathways to overcome these limitations. These innovations offer more personalized approaches with potentially fewer adverse effects and reduced resistance compared to traditional androgen-focused therapies. Novel target sites and pathways, either suppressed or overexpressed, offer control points for modulating signaling in prostate diseases, suggesting future potential for treatment through innovative exogenous substances. Data was compiled from Google Scholar, PubMed, and Google to highlight the comparative potential of these emerging methods in enhancing treatment efficacy for prostate health.

A Distinguished Roadmap of Fibroblast Senescence in Predicting Immunotherapy Response and Prognosis Across Human Cancers

The resistance of tumors to immune checkpoint inhibitors (ICI) may be intricately linked to cellular senescence, although definitive clinical validation remains elusive. In this study, comprehensive pan-cancer scRNA-seq analyses identify fibroblasts as exhibiting the most pronounced levels of cellular senescence among tumor-associated cell populations. To elucidate this phenomenon, a fibroblast senescence-associated transcriptomic signature (FSS), which correlated strongly with protumorigenic signaling pathways and immune dysregulation that fosters tumor progression, is developed. Leveraging the FSS, the machine learning (ML) framework demonstrates exceptional accuracy in predicting ICI response and survival outcomes, achieving superior area under curve (AUC) values across validation, testing, and in-house cohorts. Strikingly, FSS consistently outperforms established signatures in predictive robustness across diverse cancer subtypes. From an integrative analysis of 17 CRISPR/Cas9 libraries, CDC6 emerges as a pivotal biomarker for pan-cancer ICI response and prognostic stratification. Mechanistically, experimental evidence reveals that CDC6 in tumor cells orchestrates fibroblast senescence via TGF-β1 secretion and oxidative stress, subsequently reprogramming the tumor microenvironment and modulating ICI response. These findings underscore the translational potential of targeting fibroblast senescence as a novel therapeutic strategy to mitigate immune resistance and enhance antitumor efficacy.

Single-Cell Analysis Dissects the Effects of Vitamin D on Genetic Senescence Signatures Across Murine Tissues

Background/Objectives: Vitamin D (VD) plays a crucial role in age-related diseases, and its influence on cellular senescence (CS) could help clarify its function in aging. Considering VD's pleiotropic effects and the heterogeneity of CS. Methods: we utilized single-cell RNA sequencing (scRNA-seq) to explore these dynamics across multiple tissues. We analyzed three murine tissue datasets (bone, prostate, and skin) obtained from public repositories, enriching for senescence gene signatures. We then inferred gene regulatory networks (GRNs) at the tissue and cell-type levels and performed two cell communication analyses: one for senescent cells and another for interactions between senescent and non-senescent cells. Results: VD supplementation significantly decreased senescence scores in the skin (p = 3.96×10-134) and prostate (p=1.56×10-34). GRN analysis of the prostate revealed an altered macrophage-fibroblast regulatory relationship. In bone, distinct aging-related modules emerged for different bone lineages. In skin, contrary differentiation patterns between suprabasal and basal cells were observed. The main VD-modulated pathways were involved in inflammation, extracellular matrix remodeling, protein metabolism, and translation. VD reduced fibroblast-macrophage interactions in the prostate and skin but increased overall cellular crosstalk in bone. Conclusions: Our findings demonstrate that VD alleviates CS burden across tissues by modulating inflammation and metabolic processes and promoting differentiation. Key aging-related genes modulated by VD were linked to anabolism and cellular differentiation, suggesting VD's potential for therapeutic interventions targeting age-related diseases.

Identification the Cellular Senescence Associated lncRNA LINC01579 in Gastric Cancer

Cellular senescence is a key promoter of tumorigenesis and malignant progression. This study aimed to develop a predictive model for assessing cellular senescence in gastric cancer (GC) outcomes. We identified senescence-related genes and lncRNAs from 375 stomach adenocarcinoma (STAD) patients and established a prognostic senescence score using multivariate Cox regression, validated in testing, TCGA-STAD and the combined TCGA-COAD and READ cohorts. The model's predictive efficacy was evaluated across clinical subgroups, tumour microenvironments and immune cell infiltration. A total of 116 senescence-related lncRNAs were filtered, and patients were clustered into two senescent subtypes. The lncRNA signature identified LINC01579 as an independent prognostic factor for GC. Low-risk groups showed prolonged overall survival, increased immune cell infiltration and reduced mutation load. Downregulation of LINC01579 using antisense oligonucleotides (ASOs) on normal human fibroblasts decreased cellular proliferation and migration in GC. Collectively, this study established and validated a promising prognostic model connecting senescence-related lncRNAs and clinical outcome in GC and provided potential senescence-related biomarkers for GC prognosis prediction.

Integrative Proteomics-Metabolomics of In Vitro Degeneration of Cardiovascular Cell Lines

Long-term cell culture is an important biological approach but is also characterized by degeneration in cellular morphology, proliferation rate, and function. To explore this phenomenon in a systematic way, we conducted an integrative proteomics-metabolomics measurement of two cardiovascular cell lines of AC16 and HUVECs. The 18th culturing passages, i.e., G18, showed as the turning points by cell metabolism profiles, in which the metabolomic changes demonstrated the dysfunction of energy, amino acid, and ribonucleotide metabolism metabolic pathways. Although active protein networks showed mitochondria abundance AC16 and oxidative/nitrative sensitive HUVECs indicated the different degeneration patterns, the G18 and G30 proteomics evidenced the senescence by processes of signal transduction, signaling by interleukins, programmed cell death, cellular responses to stimuli, cell cycle, mRNA splicing, and translation. Some crucial proteins (RPS8, HNRNPR, SOD2, LMNB1, PSMA1, DECR1, GOT2, OGDH, PNP, CBS, ATIC, and IMPDH2) and metabolites (L-glutamic acid, guanine, citric acid, guanosine, guanosine diphosphate, glucose 6-phosphate, and adenosine) that contributed to the dysregulation of cellular homeostasis are identified by using the integrative proteomic-metabolomic analysis, which highlighted the increased cellular instability. These findings illuminate some vital molecular processes when culturing serial passages, which contribute holistic viewpoints of in vitro biology with emphasis on the replicative senescence of cardiovascular cells.

Cellular Senescence Genes as Cutting-Edge Signatures for Abdominal Aortic Aneurysm Diagnosis: Potential for Innovative Therapeutic Interventions

Abdominal aortic aneurysm (AAA) is the most prevalent dilated arterial aneurysm that poses a significant threat to older adults, but the molecular mechanisms linking senescence to AAA progression remain poorly understood. This study aims to identify cellular senescence-related genes (SRGs) implicated in AAA development and assess their potential as therapeutic targets. Four hundred and twenty-nine differentially expressed genes (DEGs) were identified from the GSE57691 training set, and 867 SRGs were obtained. Through the intersection of DEGs with SRGs, 19 differentially expressed senescence-related genes (DESRGs) were uncovered. Functional enrichment analysis was performed to explore their biological roles in AAA. To identify hub genes, we applied machine learning algorithms, including LASSO, SVM-RFE and random forest. These hub genes were then validated in two independent datasets. In the initial validation cohort, significant differences in the expression levels of BTG2, ETS1, ID1 and ITPR3 were observed between the AAA and control groups. Receiver operating characteristic (ROC) analysis demonstrated a robust diagnostic performance. Further validation across different AAA stages (small, large and ruptured AAA) identified ETS1 and ITPR3 as potential diagnostic genes. Subsequently, the diagnostic relevance of ETS1 and ITPR3 was further validated in human serum samples and mouse models of AAA. In addition, single-cell RNA sequencing suggests that senescent endothelial cells play a pivotal role in AAA progression, we further confirmed the correlation between ETS1 and ITPR3 and senescent endothelial cells by WB, IF and RT-qPCR. In conclusion, our study reveals the pivotal role of cellular senescence in AAA progression and identifies ETS1 and ITPR3 as promising diagnostic biomarkers.

Development and experimental validation of a senescence-related long non-coding RNA signature for prognostic prediction and immune microenvironment characterization in gastric cancer patients

Background

Cellular senescence is considered a new marker of cancer. It has been suggested that long non-coding RNA (lncRNA) can be used to predict the prognosis of cancers. However, it remains to be seen whether the lncRNAs associated with cellular senescence can be used to predict the prognosis of gastric cancer (GC). The present study aimed to develop a novel senescence-related lncRNA signature (SenLncSig) to predict GC prognosis. The SenLncSig model holds promise for enhancing patient stratification, enabling more precise prognostic predictions and facilitating immunotherapy strategies.

Methods

Senescence-associated lncRNAs were identified from RNA expression profiles in The Cancer Genome Atlas (TCGA) database through the construction of a co-expression network linking senescence genes and lncRNAs. A prognostic signature for GC (334 patients from TCGA-STAD data set), comprising the senescence-related lncRNAs, was developed through univariate and multivariate Cox proportional hazards regression analyses. By using the median SenLncSig risk score, the GC patients were categorized into high- and low-risk groups. A Kaplan-Meier analysis and gene set enrichment analysis were conducted, and immune infiltration, the tumor mutation burden (TMB), and pharmacological treatments were compared between the high- and low-risk groups. We used an independent GC cohort (an external cohort of 30 pairs of tumor and non-tumor tissues from the GC patients) and three GC cell lines to conduct a quantitative reverse-transcription polymerase chain reaction (qRT-PCR) analysis to validate the results.

Results

We established a SenLncSig, a prognostic risk model comprising the following five senescence-associated lncRNAs; AP000695.2, LINC02381, AC005586.1, AP003392.1, and AP001528.2. According to the SenLncSig, high-risk scores were associated with poor overall survival (multivariate Cox proportional hazard ratio: 1.498, 95% confidence interval: 1.294-1.735; P<0.001). The time-dependent receiver operating characteristic curve indicated that the model performed (area under the curve: 0.711). We developed a nomogram incorporating age, gender, grade, stage, T stage, M stage, N stage, and SenLncSig risk score to estimate 1-year, 3-year, and 5-year survival rates. Further, according to the results of the mutation analysis, patients with a high TMB in the high-risk group had the worst prognosis. Interestingly, the high-risk group had a stronger infiltration of regulatory T cells (P<0.001) and M2 macrophage cells (P<0.001), as well as higher tumor immune dysfunction and exclusion scores than the low-risk group. These results might explain why the high-risk group had a worse prognosis. Finally, the qRT-PCR validation revealed that the AP000695.2 and AP003392.1 expression levels were significantly higher in the tumor tissues and GC cell lines than the normal tissues and normal human gastric epithelial cell line, whereas the opposite pattern was found for LINC02381.

Conclusions

The development of the SenLncSig provided a potential tool for improving patient prognosis predictions and offered preliminary insights into predicting the efficacy of GC immunotherapy.

A machine learning approach identifies cellular senescence on transcriptome data of human cells in vitro

Although cellular senescence has been recognized as a hallmark of aging, it is challenging to detect senescence cells (SnCs) due to their high level of heterogeneity at the molecular level. Machine learning (ML) is likely an ideal approach to address this challenge because of its ability to recognize complex patterns that cannot be characterized by one or a few features, from high-dimensional data. To test this, we evaluated the performance of four ML algorithms including support vector machines (SVM), random forest (RF), decision tree (DT), and Soft Independent Modelling of Class Analogy (SIMCA), in distinguishing SnCs from controls based on bulk RNA sequencing data. The dataset includes 162 in vitro samples, covering three human cell types: fibroblasts, melanocytes, and keratinocytes, and three senescence inducers: irradiation, bleomycin treatment, and replication. Under tenfold and leave-one-out cross-validation, as well as independent dataset validation, all methods provided ~ 80% or higher accuracy, with SVM reaching over 99%. Similar accuracy was achieved using expert-curated gene lists, e.g., SenMayo and CellAge, instead of our algorithm-prioritized gene list using minimum redundancy-maximum relevance (mRMR). However, only a few genes overlapped between the gene sets, suggesting a wide impact of senescence on the transcriptome. Overall, our study demonstrated a proof-of-concept for identifying senescence using ML.

PML Nuclear Bodies and Cellular Senescence: A Comparative Study of Healthy and Premature Aging Syndrome Donors' Cells

Natural aging and age-related diseases involve the acceleration of replicative aging, or senescence. Multiple proteins are known to participate in these processes, including the promyelocytic leukemia (PML) protein, which serves as a core component of nuclear-membrane-less organelles known as PML nuclear bodies (PML-NBs). In this work, morphological changes in PML-NBs and alterations in PML protein localization at the transition of primary fibroblasts to a replicative senescent state were studied by immunofluorescence. The fibroblasts were obtained from both healthy donors and donors with premature aging syndromes (ataxia-telangiectasia and Cockayne syndrome). Our data showed an increase in both the size and the number of PML-NBs, along with nuclear enlargement in senescent cells, suggesting these changes could serve as potential cellular aging markers. Bioinformatic analysis demonstrated that 30% of the proteins in the PML interactome and ~45% of the proteins in the PML-NB predicted proteome are directly associated with senescence and aging processes. These proteins are hypothesized to participate in post-translational modifications and protein sequestration within PML-NBs, thereby influencing transcription factor regulation, DNA damage response, and negative regulation of apoptosis. The findings confirm the significant role of PML-NBs in cellular aging processes and open new avenues for investigating senescence mechanisms and age-associated diseases.

ROS-Induced Gingival Fibroblast Senescence: Implications in Exacerbating Inflammatory Responses in Periodontal Disease

Periodontal disease is the pathological outcome of the overwhelming inflammation in periodontal tissue. Cellular senescence has been associated with chronic inflammation in several diseases. However, the role of cellular senescence in the pathogenesis of periodontal disease remained unclear. This study aimed to investigate the role and the mechanism of cellular senescence in periodontal disease. Using single-cell RNA sequencing, we first found the upregulated level of cellular senescence in fibroblasts and endothelial cells from inflamed gingival tissue. Subsequently, human gingival fibroblasts isolated from healthy and inflamed gingival tissues were labeled as H-GFs and I-GFs, respectively. Compared to H-GFs, I-GFs exhibited a distinct cellular senescence phenotype, including an increased proportion of senescence-associated β-galactosidase (SA-β-gal) positive cells, enlarged cell morphology, and significant upregulation of p16INK4A expression. We further observed increased cellular reactive oxygen species (ROS) activity, mitochondrial ROS, and DNA damage of I-GFs. These phenotypes could be reversed by ROS scavenger NAC, which suggested the cause of cellular senescence in I-GFs. The migration and proliferation assay showed the decreased activity of I-GFs while the gene expression of senescence-associated secretory phenotype (SASP) factors such as IL-1β, IL-6, TGF-β, and IL-8 was all significantly increased. Finally, we found that supernatants of I-GF culture induced more neutrophil extracellular trap (NET) formation and drove macrophage polarization toward the CD86-positive M1 pro-inflammatory phenotype. Altogether, our findings implicate that, in the inflamed gingiva, human gingival fibroblasts acquire a senescent phenotype due to oxidative stress-induced DNA and mitochondrial damage, which in turn activate neutrophils and macrophages through the secretion of SASP factors.

Deciphering the impact of senescence in kidney transplant rejection: An integrative machine learning and multi-omics analysis via bulk and single-cell RNA sequencing

BACKGROUND

The demographic shift towards an older population presents significant challenges for kidney transplantation (KTx), particularly due to the vulnerability of aged donor kidneys to ischemic damage, delayed graft function, and reduced graft survival. KTx rejection poses a significant threat to allograft function and longevity of the kidney graft. The relationship between senescence and rejection remains elusive and controversial.

METHODS

Gene Expression Omnibus (GEO) provided microarray and single-cell RNA sequencing datasets. After integrating Senescence-Related Genes (SRGs) from multiple established databases, differential expression analysis, weighted gene co-expression network analysis (WGCNA), and machine learning algorithms were applied to identify predictive SRGs (pSRGs). A cluster analysis of rejection samples was conducted using the consensus clustering algorithm. Subsequently, we utilized multiple machine learning methods (RF, SVM, XGB, GLM and LASSO) based on pSRGs to develop the optimal Acute Rejection (AR) diagnostic model and long-term graft survival predictive signatures. Finally, we validated the role of pSRGs and senescence in kidney rejection through the single-cell landscape.

RESULTS

Thirteen pSRGs were identified, correlating with rejection. Two rejection clusters were divided (Cluster C1 and C2). GSVA analysis of two clusters underscored a positive correlation between senescence, KTx rejection occurrence and worse graft survival. A non-invasive diagnostic model (AUC = 0.975) and a prognostic model (1- Year AUC = 0.881; 2- Year AUC = 0.880; 3- Year AUC = 0.883) for graft survival were developed, demonstrating significant predictive capabilities to early detect acute rejection and long-term graft outcomes. Single-cell sequencing analysis provided a detailed cellular-level landscape of rejection, supporting the conclusions drawn from above.

CONCLUSION

Our comprehensive analysis underscores the pivotal role of senescence in KTx rejection, highlighting the potential of SRGs as biomarkers for diagnosing rejection and predicting graft survival, which may enhance personalized treatment strategies and improve transplant outcomes.

Spatial transcriptomic landscape unveils immunoglobin-associated senescence as a hallmark of aging

To systematically characterize the loss of tissue integrity and organ dysfunction resulting from aging, we produced an in-depth spatial transcriptomic profile of nine tissues in male mice during aging. We showed that senescence-sensitive spots (SSSs) colocalized with elevated entropy in organizational structure and that the aggregation of immunoglobulin-expressing cells is a characteristic feature of the microenvironment surrounding SSSs. Immunoglobulin G (IgG) accumulated across the aged tissues in both male and female mice, and a similar phenomenon was observed in human tissues, suggesting the potential of the abnormal elevation of immunoglobulins as an evolutionarily conserved feature in aging. Furthermore, we observed that IgG could induce a pro-senescent state in macrophages and microglia, thereby exacerbating tissue aging, and that targeted reduction of IgG mitigated aging across various tissues in male mice. This study provides a high-resolution spatial depiction of aging and indicates the pivotal role of immunoglobulin-associated senescence during the aging process.

Emerging insights in senescence: pathways from preclinical models to therapeutic innovations

Senescence is a crucial hallmark of ageing and a significant contributor to the pathology of age-related disorders. As committee members of the young International Cell Senescence Association (yICSA), we aim to synthesise recent advancements in the identification, characterisation, and therapeutic targeting of senescence for clinical translation. We explore novel molecular techniques that have enhanced our understanding of senescent cell heterogeneity and their roles in tissue regeneration and pathology. Additionally, we delve into in vivo models of senescence, both non-mammalian and mammalian, to highlight tools available for advancing the contextual understanding of in vivo senescence. Furthermore, we discuss innovative diagnostic tools and senotherapeutic approaches, emphasising their potential for clinical application. Future directions of senescence research are explored, underscoring the need for precise, context-specific senescence classification and the integration of advanced technologies such as machine learning, long-read sequencing, and multifunctional senoprobes and senolytics. The dual role of senescence in promoting tissue homoeostasis and contributing to chronic diseases highlights the complexity of targeting these cells for improved clinical outcomes.

Comprehensive assessment of cellular senescence in intestinal immunity and biologic therapy response in ulcerative colitis

Ulcerative Colitis (UC) is an inflammatory disorder characterized by chronic intestinal inflammation and immune dysregulation. Despite a clear association between cellular senescence and chronic inflammation and immune dysregulation, the mechanisms underlying cellular senescence in UC remain unclear. We screened differentially expressed genes (DEGs) associated with cellular senescence in multiple UC datasets, performed immune infiltration analysis, and constructed clinical diagnostic models. Additionally, we investigated the relationship between key genes related to cellular senescence and disease remission in UC patients undergoing biologic therapy, validating their expression in a single-cell dataset. We identified six DEGs associated with cellular senescence (TWIST1, IGFBP5, MME, IFNG, ME1, FOS). Immune infiltration results indicated strong correlations of four of these genes with immune cells and pathways. Through WGCNA, GO, and KEGG analyses, we found that gene modules strongly associated with the expression of hub genes in cellular senescence were enriched in inflammation-related pathways. In the single-cell dataset, the expression of these six key genes exhibited similarities with Immune infiltration results. Additionally, we constructed a nomogram using these six genes for diagnosing UC, demonstrating good diagnostic capability and clinical efficacy. Kaplan-Meier survival analysis revealed a significant association between changes in the expression levels of these cell genes and disease remission in UC patients undergoing biologic therapy. This study utilizes bioinformatic analysis and machine learning to identify and analyze features associated with cellular senescence in multiple UC datasets. It provides insights into the role of cellular senescence in the premature onset of intestinal aging in UC and offers new perspectives for exploring novel therapeutic targets.

Integration of single-cell and spatial transcriptome sequencing identifies CDKN2A as a senescent biomarker in endothelial cells implicating hepatocellular carcinoma malignancy

PURPOSE

Highly complex tumor microenvironment makes hepatocellular carcinoma (HCC) as one of the most malignant tumors worldwide. The role of cellular senescence in HCC has been gradually recognized. The present study aimed to comprehensively elucidate the senescence-related features of HCC in single-cell and spatial dimension.

METHODS

Single-cell RNA sequencing (scRNA-Seq) data was used to clarify the heterogeneity of senescence-related genes (SRGs) among multiple cell types within HCC. Spatial transcriptome RNA sequencing (stRNA-Seq) data was used for depicting SRGs features in spatial dimension. A prognostic model based on SRGs was constructed by using of bulk sequencing (bulk-Seq) data of HCC. The cell-cell interaction of senescent endothelial cells (ECs) in tumor microenvironment was analyzed. Then, the role of senescent ECs was verified through in vitro and in vivo experiments.

RESULTS

The level of senescence demonstrated substantial heterogeneity among different cell types within tumor microenvironment of HCC, where ECs exhibited the most prominent senescent phenotype. Senescent ECs activated specific regulatory pathways through communicating with other cell types, with a potential impact on tumor progression. Spatial analysis revealed senescent ECs mainly located in the core region of HCC. The interaction of senescent ECs and immune cells implicated their role in tumor progression and immunotherapeutic response. In addition, CDKN2A was identified as an independent risk factor for HCC prognosis by constructing a prognostic model. Patients with high risk displayed an even worse outcome. The experimental verification indicated senescence of ECs determined by CDKN2A exhibited a secretory phenotype. Furthermore, senescent ECs with CDKN2A overexpression promote the proliferation and migration of HCC.

CONCLUSION

The present study recognizes the critical effect of senescent ECs defined by CDKN2A in the promotion of tumor progression, which sheds new light on the investigation of ECs senescence in HCC.

Therapeutic targeting of senescent cells in the CNS

Senescent cells accumulate throughout the body with advanced age, diseases and chronic conditions. They negatively impact health and function of multiple systems, including the central nervous system (CNS). Therapies that target senescent cells, broadly referred to as senotherapeutics, recently emerged as potentially important treatment strategies for the CNS. Promising therapeutic approaches involve clearing senescent cells by disarming their pro-survival pathways with 'senolytics'; or dampening their toxic senescence-associated secretory phenotype (SASP) using 'senomorphics'. Following the pioneering discovery of first-generation senolytics dasatinib and quercetin, dozens of additional therapies have been identified, and several promising targets are under investigation. Although potentially transformative, senotherapies are still in early stages and require thorough testing to ensure reliable target engagement, specificity, safety and efficacy. The limited brain penetrance and potential toxic side effects of CNS-acting senotherapeutics pose challenges for drug development and translation to the clinic. This Review assesses the potential impact of senotherapeutics for neurological conditions by summarizing preclinical evidence, innovative methods for target and biomarker identification, academic and industry drug development pipelines and progress in clinical trials.

Immunosuppressive SOX9-AS1 Resists Triple-Negative Breast Cancer Senescence Via Regulating Wnt Signalling Pathway

Long noncoding RNAs (lncRNAs) are involved in the regulation of triple-negative breast cancer (TNBC) senescence, while pro-carcinogenic lncRNAs resist senescence onset leading to the failure of therapy-induced senescence (TIS) strategy, urgently identifying the key senescence-related lncRNAs (SRlncRNAs). We mined seven SRlncRNAs (SOX9-AS1, LINC01152, AC005152.3, RP11-161 M6.2, RP5-968 J1.1, RP11-351 J23.1 and RP11-666A20.3) by bioinformatics, of which SOX9-AS1 was reported to be pro-carcinogenic. In vitro experiments revealed the highest expression of SOX9-AS1 in MDA-MD-231 cells. SOX9-AS1 knockdown inhibited cell growth (proliferation, cycle and apoptosis) and malignant phenotypes (migration and invasion), while SOX9-AS1 overexpression rescued these effects. Additionally, SOX9-AS1 knockdown facilitated tamoxifen-induced cellular senescence and the transcription of senescence-associated secretory phenotype (SASP) factors (IL-1α, IL-1β, IL-6 and IL-8) mechanistically by resisting senescence-induced Wnt signal (GSK-3β/β-catenin) activation. Immune infiltration analysis revealed that low SOX9-AS1 expression was accompanied by a high infiltration of naïve B cells, CD8+ T cells and γδ T cells. In conclusion, SOX9-AS1 resists TNBC senescence via regulating the Wnt signalling pathway and inhibits immune infiltration. Targeted inhibition of SOX9-AS1 enhances SASP and thus mobilises immune infiltration to adjunct TIS strategy.

Pan-cancer characterization of cellular senescence reveals its inter-tumor heterogeneity associated with the tumor microenvironment and prognosis

Cellular senescence (CS) is characterized by the irreversible cell cycle arrest and plays a key role in aging and diseases, such as cancer. Recent years have witnessed the burgeoning exploration of the intricate relationship between CS and cancer, with CS recognized as either a suppressing or promoting factor and officially acknowledged as one of the 14 cancer hallmarks. However, a comprehensive characterization remains absent from elucidating the divergences of this relationship across different cancer types and its involvement in the multi-facets of tumor development. Here we systematically assessed the cellular senescence of over 10,000 tumor samples from 33 cancer types, starting by defining a set of cancer-associated CS signatures and deriving a quantitative metric representing the CS status, called CS score. We then investigated the CS heterogeneity and its intricate relationship with the prognosis, immune infiltration, and therapeutic responses across different cancers. As a result, cellular senescence demonstrated two distinct prognostic groups: the protective group with eleven cancers, such as LIHC, and the risky group with four cancers, including STAD. Subsequent in-depth investigations between these two groups unveiled the potential molecular and cellular mechanisms underlying the distinct effects of cellular senescence, involving the divergent activation of specific pathways and variances in immune cell infiltrations. These results were further supported by the disparate associations of CS status with the responses to immuno- and chemo-therapies observed between the two groups. Overall, our study offers a deeper understanding of inter-tumor heterogeneity of cellular senescence associated with the tumor microenvironment and cancer prognosis.

Deoxyarbutin targets mitochondria to trigger p53-dependent senescence of glioblastoma cells

Cellular senescence is a natural barrier of the transition from premalignant cells to invasive cancer. Pharmacological induction of senescence has been proposed as a possible anticancer strategy. In this study, we found that deoxyarbutin inhibited the growth of glioblastoma (GBM) cells by inducing cellular senescence, independent of tyrosinase expression. Instead, deoxyarbutin induced mitochondrial oxidative stress and damage. These aberrant mitochondria were key to the p53-dependent senescence of GBM cells. Facilitating autophagy or mitigating mitochondrial oxidative stress both suppressed p53 expression and alleviated cellular senescence induced by deoxyarbutin. Thus, our study reveals that deoxyarbutin induces mitochondrial oxidative stress to trigger the p53-dependent senescence of GBM cells. Importantly, deoxyarbutin treatment resulted in accumulation of p53, induction of cellular senescence, and inhibition of tumor growth in a subcutaneous tumor model of mouse. In conclusion, our study reveals that deoxyarbutin has therapeutic potential for GBM by inducing mitochondrial oxidative stress for p53-dependent senescence of GBM cells.

Oxidative stress-induced gene expression changes in prostate epithelial cells in vitro reveal a robust signature of normal prostatic senescence and aging

Oxidative stress has long been postulated to play an essential role in aging mechanisms, and numerous forms of molecular damage associated with oxidative stress have been well documented. However, the extent to which changes in gene expression in direct response to oxidative stress are related to actual cellular aging, senescence, and age-related functional decline remains unclear. Here, we ask whether H2O2-induced oxidative stress and resulting gene expression alterations in prostate epithelial cells in vitro reveal gene regulatory changes typically observed in naturally aging prostate tissue and age-related prostate disease. While a broad range of significant changes observed in the expression of non-coding transcripts implicated in senescence-related responses, we also note an overrepresentation of gene-splicing events among differentially expressed protein-coding genes induced by H2O2. Additionally, the collective expression of these H2O2-induced DEGs is linked to age-related pathological dysfunction, with their protein products exhibiting a dense network of protein-protein interactions. In contrast, co-expression analysis of available gene expression data reveals a naturally occurring highly coordinated expression of H2O2-induced DEGs in normally aging prostate tissue. Furthermore, we find that oxidative stress-induced DEGs statistically overrepresent well-known senescence-related signatures. Our results show that oxidative stress-induced gene expression in prostate epithelial cells in vitro reveals gene regulatory changes typically observed in naturally aging prostate tissue and age-related prostate disease.

Senescence Reprogramming by MTHFD2 Deficiency Facilitates Tumor Progression

Background: Age is a critical risk factor for cancer, as its incidence and mortality increase with age. However, there is limited understanding of the molecular changes aging induces in tumors. Methods: We explored demographic differences between young and old cancer patients and identified age sixty and above as pivotal in cancer prognosis. Subsequently, we developed an aging-related prognostic model based on genes to assess senescence's impact on aging-associated cancer. Grounded in the coefficients and expression levels of these identified signature genes, a risk score was computed, enabling the classification of collected samples into aging-related high-risk and low-risk cohorts. Results: Our study revealed increased genomic instability and somatic mutations in tumors from older individuals. We also found alterations in carcinogenic signaling pathways, particularly immune responses, inflammatory pathways, and cell cycle arrest in susceptible populations. Single-cell RNA sequencing showed heightened frequencies of exhausted T cells, myeloid cells, and B cells in high-risk cohorts. Conclusion: MTHFD2 emerged as a crucial molecular switch regulating senescence in cancer. Its deletion promoted tumor growth by inducing cell senescence and stimulating the senescence-associated secretory phenotype (SASP) in senescent tumor cells. This highlights the need for tailored methodologies in effective cancer management.

CDKN1A as a target of senescence in heart failure: insights from a multiomics study

Background

Cardiomyocyte senescence plays a crucial role as a pathological mechanism in heart failure (HF). However, the exact triggering factors and underlying causes of HF onset and progression are still not fully understood.

Objectives

By integrating multi-omics data, this study aimed to determine the genetic associations between cardiomyocyte and HF using cell senescence-related genes (SRGs).

Methods

The study utilized the CellAge database and the SenMayo dataset, combined with high-resolution single-cell RNA sequencing (scRNA-seq) data, to identify SRG and examine differences in cardiac cell expression. To explore the causal relationship with HF using Mendelian Randomization (MR). Genetic variations influencing gene expression, DNA methylation, and protein expression (cis-eQTL, cis-mQTL, and cis-pQTL) were analyzed using the two-sample MR (TSMR) and summary-data-based MR (SMR). Additionally, Bayesian colocalization analysis, germline genetic variation, and bulk RNA data were employed to strengthen the reliability of the results. The application potential of therapeutic targets is ultimately assessed by evaluating their druggability.

Results

The expression of 39 SRGs in cardiomyocytes was identified. In the discovery set revealed that CDKN1A (OR = 1.09, 95% confidence interval (CI) 1.02-1.15, FDR = 0.048) could be causally related to HF, and the results are also replicated in the validation set (OR = 1.20, 95% confidence interval (CI) 1.10-1.30, FDR <0.0001). Based on the SMR method, CDKN1A was confirmed as a candidate pathogenic gene for HF, and its methylation (cg03714916, cg08179530) was associated with HF risk loci. The result is validated by Bayesian colocalization analysis, genetic variations, and bulk RNA data. The druggability analysis identified two potential therapeutic drugs.

Conclusion

Based on multi-omics data, this study uncovered the reciprocal regulation of cardiomyocyte senescence through CDKN1A, providing potential targets for HF drug development.

Recovering single-cell expression profiles from spatial transcriptomics with scResolve

Many popular spatial transcriptomics techniques lack single-cell resolution. Instead, these methods measure the collective gene expression for each location from a mixture of cells, potentially containing multiple cell types. Here, we developed scResolve, a method for recovering single-cell expression profiles from spatial transcriptomics measurements at multi-cellular resolution. scResolve accurately restores expression profiles of individual cells at their locations, which is unattainable with cell type deconvolution. Applications of scResolve on human breast cancer data and human lung disease data demonstrate that scResolve enables cell-type-specific differential gene expression analysis between different tissue contexts and accurate identification of rare cell populations. The spatially resolved cellular-level expression profiles obtained through scResolve facilitate more flexible and precise spatial analysis that complements raw multi-cellular level analysis.

Identification of senescence-related genes for potential therapeutic biomarkers of atrial fibrillation by bioinformatics, human histological validation, and molecular docking

Background

Cellular senescence is pivotal in the occurrence and progression of atrial fibrillation (AF). This study aimed to identify senescence-related genes that could be potential therapeutic biomarkers for AF.

Methods

AF-related differentially expressed genes (DEGs) were identified using the Gene Expression Omnibus dataset. Weighted gene co-expression network analysis (WGCNA) was used to analyze important modules and potential hub genes. Integrating senescence-related genes, potential biomarkers were identified. Their differential expression levels were then validated in human atrial tissue, HL-1 cells, and Angiotensin II-infused mice. Finally, molecular docking analysis was conducted to predict potential interactions between potential biomarkers and the senolytic drug Navitoclax.

Results

We identified seven genes common to AF-related DEGs and senescence-related genes. Three significant modules were selected from WGCNA analysis. Taken together, three senescence-related genes (ETS1, SP1, and WT1) were found to be significantly associated with AF. Protein-protein interaction network analysis revealed biological connections among the predicted target genes of ETS1, SP1, and WT1. Notably, ETS1, SP1, and WT1 exhibited significant differential expression in clinical samples as well as in vitro and in vivo models. Molecular docking revealed favorable binding affinity between senolytic Navitoclax and these potential biomarkers.

Conclusions

This study highlights ETS1, SP1, and WT1 as crucial senescence-related genes associated with AF, offering potential therapeutic targets, with supportive evidence of binding affinity with senolytic Navitoclax. These findings provide novel insights into AF pathogenesis from a senescence perspective.