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Ageing is a complex biological process in which a gradual decline in physiological fitness increases susceptibility to diseases such as neurodegenerative disorders and cancer. Cellular senescence, a state of irreversible cell-growth arrest accompanied by functional deterioration, has emerged as a pivotal driver of ageing. In this Review, we discuss how heterochromatin loss, telomere attrition and DNA damage contribute to cellular senescence, ageing and age-related diseases by eliciting genome instability, innate immunity and inflammation. We also discuss how emerging therapeutic strategies could restore heterochromatin stability, maintain telomere integrity and boost the DNA repair capacity, and thus counteract cellular senescence and ageing-associated pathologies. Finally, we outline current research challenges and future directions aimed at better comprehending and delaying ageing., Competing Interests: Competing interests: The authors declare no competing interests., (© 2024. Springer Nature Limited.)

Background: Observational studies about the association between coronavirus disease 2019 (COVID-19) vaccination and thrombosis/ischemic stroke are inconsistent. The aim of this study is to assess the causality between COVID-19 vaccination and thrombosis-related biomarkers/thrombosis/ischemic stroke using mendelian randomization (MR) analysis., Methods: A two-sample MR analysis using publicly available genome-wide association study (GWAS) data was conducted. Causal effects were appraised using inverse variance weighted (IVW, as a primary method), with supplementary methods including constrained maximum likelihood and model averaging, MR-Robust Adjusted Profile Score, MR-Egger regression, simple mode, weighted median, and weighted mode. Sensitivity analyses were conducted using Cochran's Q test, MR-Egger intercept test, and leave-one-out analysis., Results: Genetically predicted COVID-19 vaccination was negatively associated with C-C motif chemokine 3 [CCL3, odds ratio (OR): 0.694, 95% confidence intervals (CI): 0.484-0.995] and multiple coagulation factor deficiency protein 2 (MCFD2, OR: 0.806, 95% CI: 0.675-0.963). Meanwhile, the IVW analysis revealed significant causal effects between genetically predicted COVID-19 vaccination and ischemic stroke (OR: 1.088, 95% CI: 1.006-1.177), large artery stroke (LAS, OR: 1.251, 95% CI: 1.028-1.521). The leave-one-out analysis revealed that no individual SNP exerted a significant effect on the overall causal estimate., Conclusion: Our study provided evidence supporting a potential causal association of genetically predicted COVID-19 vaccination with CCL3 levels, MCFD2 levels, ischemic stroke risk and LAS risk. These results provide preliminary evidence of potential adverse associations, but further studies are required to fully understand the mechanisms and to validate these findings across broader populations., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier Inc.)

Dysfunction of the ribosome manifests during cellular senescence and contributes to tissue aging, functional decline, and development of aging-related disorders in ways that have remained enigmatic. Here, we conducted a comprehensive CRISPR-based loss-of-function (LOF) screen of ribosome-associated genes (RAGs) in human mesenchymal progenitor cells (hMPCs). Through this approach, we identified ribosomal protein L22 (RPL22) as the foremost RAG whose deficiency mitigates the effects of cellular senescence. Consequently, absence of RPL22 delays hMPCs from becoming senescent, while an excess of RPL22 accelerates the senescence process. Mechanistically, we found in senescent hMPCs, RPL22 accumulates within the nucleolus. This accumulation triggers a cascade of events, including heterochromatin decompaction with concomitant degradation of key heterochromatin proteins, specifically heterochromatin protein 1γ (HP1γ) and heterochromatin protein KRAB-associated protein 1 (KAP1). Subsequently, RPL22-dependent breakdown of heterochromatin stimulates the transcription of ribosomal RNAs (rRNAs), triggering cellular senescence. In summary, our findings unveil a novel role for nucleolar RPL22 as a destabilizer of heterochromatin and a driver of cellular senescence, shedding new light on the intricate mechanisms underlying the aging process., (© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Background: To investigate the involvement of LINC02605 in the progression of paediatric Mycoplasma pneumoniae pneumonia (MPP)., Methods: One hundred and thirty-two children with MPP (90 simple MPP and 42 MPP + diarrhoea) were enrolled, and their plasma was collected for detection of LINC026505 expression. CCK-8 kit and commercial apoptosis kit were introduced to determine cell growth and apoptosis. In silico prediction analyses were conducted to predict the downstream miRNA for LINC02605, following verification by dual luciferase reporter assay. The lipid-associated membrane proteins (LAMPs) were used to treat A549 and Coca-2 cells., Results: LIN02605 was highly expressed in the MPP, especially in MPP complicated with diarrhoea. LINC02605 downregulation in A549 cells correlated with significant suppression of cell apoptosis rate and growth inhibition rate in vitro. Introduction of miR-539-5p inhibited luciferase activity in a reporter system containing the wild-type LINC02605 and CXCL1. After stimulation with LAMPs, overexpression of LINC02605 and CXCL1 and inhibition of miR-539-5p were found. miR-539-5p and CXCL1 knockdown resulted in a rescue effect on the LINC02605-inhibited cell apoptosis. LAMPs induced IL-1β in intestinal epithelial cells and IL-1β induced LINC02605 expression in A549 cells., Conclusions: LINC02605 was upregulated in MPP and miR-539-5p was a target for LINC02605. LINC02605 may be involved in the crosstalk between the gastrointestinal tract and the respiratory tract., (© 2024 Stichting European Society for Clinical Investigation Journal Foundation. Published by John Wiley & Sons Ltd.)

Sirtuins are pro-longevity genes with chromatin modulation potential, but how these properties are connected is not well understood. Here, we generated a panel of isogeneic human stem cell lines with SIRT1-SIRT7 knockouts and found that any sirtuin deficiency leads to accelerated cellular senescence. Through large-scale epigenomic analyses, we show how sirtuin deficiency alters genome organization and that genomic regions sensitive to sirtuin deficiency are preferentially enriched in active enhancers, thereby promoting interactions within topologically associated domains and the formation of de novo enhancer-promoter loops. In all sirtuin-deficient human stem cell lines, we found that chromatin contacts are rewired to promote aberrant activation of the placenta-specific gene PAPPA, which controls the pro-senescence effects associated with sirtuin deficiency and serves as a potential aging biomarker. Based on our survey of the 3D chromatin architecture, we established connections between sirtuins and potential target genes, thereby informing the development of strategies for aging interventions., Competing Interests: Declaration of interests J.C.I.B. is an employee of Altos Labs., (Copyright © 2024 Elsevier Inc. All rights reserved.)

The summer Eurasian westerly jet is reported to become weaker and wavier, thus promoting the frequent weather extremes. However, the primary driver of the changing jet stream remains in debate, mainly due to the regionality and seasonality of the Eurasian jet. Here we report a sharp increase, by approximately 140%, in the interannual variability of the summertime East Asian jet (EAJ) since the end of twentieth century. Such interdecadal change induces considerable changes in the large-scale circulation pattern across Eurasia, and consequently weather and climate extremes including heatwaves, droughts, and Asian monsoonal rainfall regime shifts. The trigger mainly emerges from preceding February North Atlantic seesaw called Scandinavian pattern (contributing to 81.1 ± 2.9% of the enhanced EAJ variability), which harnesses the "cross-seasonal-coupled oceanic-atmospheric bridge" to exert a delayed impact on EAJ and thus aids relevant predictions five months in advance. However, projections from state-of-the-art models with prescribed anthropogenic forcing exhibit no similar circulation changes. This sheds light on that, at the interannual timescale, a substantial portion of recently increasing variability in the East Asian sector of the Eurasian westerly jet arises from unforced natural variability., (© 2024. The Author(s).)

Epigenetic dysregulation emerges as a critical hallmark and driving force of aging. Although still an evolving field with much to explore, it has rapidly gained significance by providing valuable insights into the mechanisms of aging and potential therapeutic opportunities for age-related diseases. Recent years have witnessed remarkable strides in our understanding of the epigenetic landscape of aging, encompassing pivotal elements, such as DNA methylation, histone modifications, RNA modifications, and noncoding (nc) RNAs. Here, we review the latest discoveries that shed light on new epigenetic mechanisms and critical targets for predicting and intervening in aging and related disorders. Furthermore, we explore burgeoning interventions and exemplary clinical trials explicitly designed to foster healthy aging, while contemplating the potential ramifications of epigenetic influences., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2023 Elsevier Ltd. All rights reserved.)

Aging, as a complex process involving multiple cellular and molecular pathways, is known to be exacerbated by various stresses. Because responses to these stresses, such as oxidative stress and genotoxic stress, are known to interplay with the epigenome and thereby contribute to the development of age-related diseases, investigations into how such epigenetic mechanisms alter gene expression and maintenance of cellular homeostasis is an active research area. In this review, we highlight recent studies investigating the intricate relationship between stress and aging, including its underlying epigenetic basis; describe different types of stresses that originate from both internal and external stimuli; and discuss potential interventions aimed at alleviating stress and restoring epigenetic patterns to combat aging or age-related diseases. Additionally, we address the challenges currently limiting advancement in this burgeoning field., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2023 Elsevier Inc. All rights reserved.)

Ageing is a critical factor in spinal-cord-associated disorders 1 , yet the ageing-specific mechanisms underlying this relationship remain poorly understood. Here, to address this knowledge gap, we combined single-nucleus RNA-sequencing analysis with behavioural and neurophysiological analysis in non-human primates (NHPs). We identified motor neuron senescence and neuroinflammation with microglial hyperactivation as intertwined hallmarks of spinal cord ageing. As an underlying mechanism, we identified a neurotoxic microglial state demarcated by elevated expression of CHIT1 (a secreted mammalian chitinase) specific to the aged spinal cords in NHP and human biopsies. In the aged spinal cord, CHIT1-positive microglia preferentially localize around motor neurons, and they have the ability to trigger senescence, partly by activating SMAD signalling. We further validated the driving role of secreted CHIT1 on MN senescence using multimodal experiments both in vivo, using the NHP spinal cord as a model, and in vitro, using a sophisticated system modelling the human motor-neuron-microenvironment interplay. Moreover, we demonstrated that ascorbic acid, a geroprotective compound, counteracted the pro-senescent effect of CHIT1 and mitigated motor neuron senescence in aged monkeys. Our findings provide the single-cell resolution cellular and molecular landscape of the aged primate spinal cord and identify a new biomarker and intervention target for spinal cord degeneration., (© 2023. The Author(s), under exclusive licence to Springer Nature Limited.)

Our understanding of the molecular basis for cellular senescence remains incomplete, limiting the development of strategies to ameliorate age-related pathologies by preventing stem cell senescence. Here, we performed a genome-wide CRISPR activation (CRISPRa) screening using a human mesenchymal precursor cell (hMPC) model of the progeroid syndrome. We evaluated targets whose activation antagonizes cellular senescence, among which SOX5 outperformed as a top hit. Through decoding the epigenomic landscapes remodeled by overexpressing SOX5, we uncovered its role in resetting the transcription network for geroprotective genes, including HMGB2. Mechanistically, SOX5 binding elevated the enhancer activity of HMGB2 with increased levels of H3K27ac and H3K4me1, raising HMGB2 expression so as to promote rejuvenation. Furthermore, gene therapy with lentiviruses carrying SOX5 or HMGB2 rejuvenated cartilage and alleviated osteoarthritis in aged mice. Our study generated a comprehensive list of rejuvenators, pinpointing SOX5 as a potent driver for rejuvenation both in vitro and in vivo., Competing Interests: Declaration of interests C.R.E., P.R., S.H., and J.C.I.B. are employees of Altos Labs., (Copyright © 2023 Elsevier Inc. All rights reserved.)

Hepatocellular carcinoma (HCC) is a leading cause of cancer-related mortality worldwide. The in-depth study of genes and metabolites related to nucleotide metabolism will provide new ideas for predicting the prognosis of HCC patients. This study integrated the transcriptome data of different cancer types to explore the characteristics and significance of nucleotide metabolism-related genes (NMGRs) in different cancer types. Then, we constructed a new HCC classifier and prognosis model based on HCC samples from TCGA and GEO, and detected the gene expression level in the model through molecular biology experiments. Finally, nucleotide metabolism-related products in serum of HCC patients were examined using untargeted metabolomics. A total of 97 NMRGs were obtained based on bioinformatics techniques. In addition, a clinical model that could accurately predict the prognostic outcome of HCC was constructed, which contained 11 NMRGs. The results of PCR experiments showed that the expression levels of these genes were basically consistent with the predicted trends. Meanwhile, the results of untargeted metabolomics also proved that there was a significant nucleotide metabolism disorder in the development of HCC. Our results provide a promising insight into nucleotide metabolism in HCC, as well as a tailored prognostic and chemotherapy sensitivity prediction tool for patients.

Objective: Considering that there are no effective biomarkers for the screening of cardia gastric cancer (CGC), we developed a noninvasive diagnostic approach, employing data-independent acquisition (DIA) proteomics to identify candidate protein markers., Methods: Plasma samples were obtained from 40 subjects, 10 each for CGC, cardia high-grade dysplasia (CHGD), cardia low-grade dysplasia (CLGD), and healthy controls. Proteomic profiles were obtained through liquid chromatography-mass spectrometry (LC-MS/MS-based DIA proteomics. Candidate plasma proteins were identified by weighted gene co-expression network analysis (WGCNA) combined with machine learning and further validated by the Human Protein Atlas (HPA) database. The area under the receiver operating characteristic curve (AUC) was used to evaluate the performance of the biomarker panel., Results: There was a clear distinction in proteomic features among CGC, CHGD, CLGD, and the healthy controls. According to the WGCNA, we found 42 positively associated and 164 inversely associated proteins related to CGC progression and demonstrated several canonical cancer-associated pathways. Combined with the results from random forests, LASSO regression, and immunohistochemical results from the HPA database, we identified three candidate proteins (GSTP1, CSRP1, and LY6G6F) that could together distinguish CLGD (AUC = 0.91), CHGD (AUC = 0.99) and CGC (AUC = 0.98) from healthy controls with excellent accuracy., Conclusions: The panel of protein biomarkers showed promising diagnostic potential for CGC and precancerous lesions. Further validation and a larger-scale study are warranted to assess its potential clinical applications, suggesting a potential avenue for CGC prevention in the future., Competing Interests: The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Author Zeming Wu serves as a technical advisor for “iPhenome Biotechnology (Dalian)” company. In the Methods section of the manuscript, he provided recommendations for bioinformatics analysis. There are no financial relationships or conflicts of interest between the author's affiliation and “iPhenome Biotechnology (Dalian)” company. This study did not receive any form of funding or support from “iPhenome Biotechnology (Dalian)” company. The research results are objective and truthful, and Zeming Wu's involvement did not influence the authenticity of the results. Other authors declare that they have no conflict of interests., (© 2023 Chinese National Cancer Center. Published by Elsevier B.V.)

N 6 -methyladenosine (m 6 A) is a dynamic and reversible RNA modification that has emerged as a crucial player in the life cycle of RNA, thus playing a pivotal role in various biological processes. In recent years, the potential involvement of RNA m 6 A modification in aging and age-related diseases has gained increasing attention, making it a promising target for understanding the molecular mechanisms underlying aging and developing new therapeutic strategies. This Perspective article will summarize the current advances in aging-related m 6 A regulation, highlighting the most significant findings and their implications for our understanding of cellular senescence and aging, and the potential for targeting RNA m 6 A regulation as a therapeutic strategy. We will also discuss the limitations and challenges in this field and provide insights into future research directions. By providing a comprehensive overview of the current state of the field, this Perspective article aims to facilitate further advances in our understanding of the molecular mechanisms underlying aging and to identify new therapeutic targets for aging-related diseases., (© 2023 The Authors. Aging Cell published by Anatomical Society and John Wiley & Sons Ltd.)

N 6 -methyladenosine (m 6 A), the most prevalent mRNA modification in eukaryotic cells, is known to play regulatory roles in a wide array of biological processes, including aging and cellular senescence. To investigate such roles, the m 6 A modification can be identified across the entire transcriptome by immunoprecipitation of methylated RNA with an anti-m 6 A antibody, followed by high-throughput sequencing (meRIP-seq or m 6 A-seq). Presented here is a protocol for employing meRIP-seq to profile the RNA m 6 A landscape in senescent human cells. We described, in detail, sample preparation, mRNA isolation, immunoprecipitation, library preparation, sequencing, bioinformatic analysis and validation. We also provided tips and considerations for the optimization and interpretation of the results. Our protocol serves as a methodological resource for investigating transcriptomic m 6 A alterations in cellular senescence as well as a valuable paradigm for the validation of genes of interest., (© 2013-2023 The Journal of Biological Methods, All rights reserved.)

The primate frontal lobe (FL) is sensitive to aging-related neurocognitive decline. However, the aging-associated molecular mechanisms remain unclear. Here, using physiologically aged non-human primates (NHPs), we depicted a comprehensive landscape of FL aging with multidimensional profiling encompassing bulk and single-nucleus transcriptomes, quantitative proteome, and DNA methylome. Conjoint analysis across these molecular and neuropathological layers underscores nuclear lamina and heterochromatin erosion, resurrection of endogenous retroviruses (ERVs), activated pro-inflammatory cyclic GMP-AMP synthase (cGAS) signaling, and cellular senescence in post-mitotic neurons of aged NHP and human FL. Using human embryonic stem-cell-derived neurons recapitulating cellular aging in vitro, we verified the loss of B-type lamins inducing resurrection of ERVs as an initiating event of the aging-bound cascade in post-mitotic neurons. Of significance, these aging-related cellular and molecular changes can be alleviated by abacavir, a nucleoside reverse transcriptase inhibitor, either through direct treatment of senescent human neurons in vitro or oral administration to aged mice., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)

Background: Chlamydia psittaci is a small bacterium often found in birds, including poultry, and domesticated mammals, which causes psittacosis (or parrot fever) in humans. Different strains of C. psittaci respond variably to antibiotics, suggesting a possible risk of antibiotic resistance. In general, different genotypes of C. psittaci have relatively stable hosts and different pathogenicity., Methods: Macrogenomic sequencing was performed using nucleic acids extracted from psittacosis patients' alveolar lavage fluid samples and analyzed for genetic variability and antibiotic resistance genes. Nucleic acid amplification sequences specific to the core coding region of the C. psittaci ompA gene were used, and a phylogenetic tree was constructed with C. psittaci genotypic sequences from other sources, including Chinese published sources. The C. psittaci found in each patient were genotyped by comparing ompA gene sequences. In addition, to better illustrate the relationship between genotype and host of C. psittaci , 60 bird fecal samples were collected from bird-selling stores for screening and C. psittaci typing., Results: Macrogenomic sequence alignment revealed the presence of resistance genes in varying abundance in samples from all three patients, including C. psittaci resistance gene sequences from two patients that matched those previously published on NCBI. Based on ompA genotyping, two patients were infected with C. psittaci genotype A and one patient was infected with genotype B. All five C. psittaci -positive samples obtained from bird-selling stores were genotype A. Both genotypes are reported to be infectious to humans. The host origin of the samples and the previously reported main sources of each genotype suggested that all but one of the C. psittaci genotype A in this study were derived from parrots, while genotype B was probably derived from chickens., Conclusion: The presence of bacterial resistance genes in psittacosis patients may affect the efficacy of clinical antibiotic therapy. Focusing on the developmental progression of bacterial resistance genes and differences in the therapeutic efficacy may facilitate effective treatment of clinical bacterial infections. Pathogenicity genotypes (e.g., genotype A and genotype B) are not limited to one animal host, suggesting that monitoring the development and changes of C. psittaci may help prevent transmission to humans., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Lu, Yuan, Wu, Wang, Wu, Chen, Zhang, Chen, Zou, Hu, Feng, Lu, Ji, Qiu, Xu, Jiang, Li, Peng, Bai, Cai, Geng and Shi.)

How N 6 -methyladenosine (m 6 A), the most abundant mRNA modification, contributes to primate tissue homeostasis and physiological aging remains elusive. Here, we characterize the m 6 A epitranscriptome across the liver, heart and skeletal muscle in young and old nonhuman primates. Our data reveal a positive correlation between m 6 A modifications and gene expression homeostasis across tissues as well as tissue-type-specific aging-associated m 6 A dynamics. Among these tissues, skeletal muscle is the most susceptible to m 6 A loss in aging and shows a reduction in the m 6 A methyltransferase METTL3. We further show that METTL3 deficiency in human pluripotent stem cell-derived myotubes leads to senescence and apoptosis, and identify NPNT as a key element downstream of METTL3 involved in myotube homeostasis, whose expression and m 6 A levels are both decreased in senescent myotubes. Our study provides a resource for elucidating m 6 A-mediated mechanisms of tissue aging and reveals a METTL3-m 6 A-NPNT axis counteracting aging-associated skeletal muscle degeneration., (© 2023. The Author(s), under exclusive licence to Springer Nature America, Inc.)

A fundamental understanding of cell shaping with confined flexible filaments, including microtubules, actin filaments, and engineered nanotubes, has been limited by the complex interplay between the cell membrane and encapsulated filaments. Here, combining theoretical modeling and molecular dynamics simulations, we investigate the packing of an open or closed filament inside a vesicle. Depending on the relative stiffness and size of the filament to the vesicle as well as the osmotic pressure, the vesicle could evolve from an axisymmetric configuration to a general configuration with a maximum of three reflection planes, and the filament could bend in or out of plane or even coil up. A plethora of system morphologies are determined. Morphological phase diagrams predicting conditions of shape and symmetry transitions are established. Organization of actin filaments or bundles, microtubules, and nanotube rings inside vesicles, liposomes, or cells are discussed. Our results provide a theoretical basis to understand cell shaping and cellular stability and to help guide the development and design of artificial cells and biohybrid microrobots.

Although the mTOR-4E-BP1 signaling pathway is implicated in aging and aging-related disorders, the role of 4E-BP1 in regulating human stem cell homeostasis remains largely unknown. Here, we report that the expression of 4E-BP1 decreases along with the senescence of human mesenchymal stem cells (hMSCs). Genetic inactivation of 4E-BP1 in hMSCs compromises mitochondrial respiration, increases mitochondrial reactive oxygen species (ROS) production, and accelerates cellular senescence. Mechanistically, the absence of 4E-BP1 destabilizes proteins in mitochondrial respiration complexes, especially several key subunits of complex III including UQCRC2. Ectopic expression of 4E-BP1 attenuates mitochondrial abnormalities and alleviates cellular senescence in 4E-BP1-deficient hMSCs as well as in physiologically aged hMSCs. These f indings together demonstrate that 4E-BP1 functions as a geroprotector to mitigate human stem cell senescence and maintain mitochondrial homeostasis, particularly for the mitochondrial respiration complex III, thus providing a new potential target to counteract human stem cell senescence., (©The Author(s) 2022. Published by Oxford University Press on behalf of Higher Education Press.)

Objective: To explore the molecular mechanism of sevoflurane-induced neurotoxicity and to determine whether lncRNA HOXA11-AS affects sevoflurane-induced neuronal apoptosis and inflammation by regulating miR-98-5p/EphA4., Methods: Morris water maze (MWM) test was used to detect the learning and memory ability of rats, HE staining was used to observe hippocampal pathology, TUNEL staining was used to detect the level of neuronal apoptosis, and RT-qPCR was used to detect the expression of HOXA11-AS, miR-98-5p, IL-6, IL-1 β , and TNF- α . At the same time, the contents of IL-6, IL-1 β , and TNF- α in serum were detected by ELISA. The expressions of apoptosis-related proteins EphA4, Bax, Cleaved caspase 3, and Bcl-2 were detected by Western blot. The dual-luciferase gene reporter verified the targeting relationship between HOXA11-AS and miR-98-5p and the targeting relationship between miR-98-5p and EphA4., Results: The expression of HOXA11-AS was observed in sevoflurane-treated rats or cells and promoted neuronal apoptosis and inflammation. HOXA11-AS was knocked out alone, or miR-98-5p was overexpressed which attenuates neuronal apoptosis and inflammatory inflammation after sevoflurane treatment. Furthermore, knockdown of HOXA11-AS alone was partially restored by knockdown of miR-98-5p or overexpression of EphA4., Conclusion: Inhibition of lncRNA HOXA11-AS attenuates sevoflurane-induced neuronal apoptosis and inflammatory responses via miR-98-5p/EphA4., Competing Interests: The authors declare that they have no conflicts of interest., (Copyright © 2023 Li Zhao et al.)

Background: More than half of the cases of fetal structural anomalies have no known cause with standard investigations like karyotype testing and chromosomal microarray. The differential metabolic profiles of amniotic fluid (AF) and maternal blood may reveal valuable information about the physiological processes of fetal development, which may provide valuable biomarkers for fetal health diagnostics., Methods: This cohort study of singleton-pregnant women had indications for amniocentesis, including structural anomalies and a positive result from maternal serum screening or non-invasive prenatal testing, but did not have any positive abnormal karyotype or chromosomal microarray analysis results. A total of 1580 participants were enrolled between June 2021 and March 2022. Of the 1580 pregnant women who underwent amniocentesis, 294 were included in the analysis. There were 137 pregnant women in the discovery cohort and 157 in the validation cohort., Results: High-coverage untargeted metabolomic analysis of AF revealed distinct metabolic signatures with 321 of the 602 metabolites measured (53%) (false discovery rate, q < 0.005), among which amino acids predominantly changed in structural anomalies. Targeted metabolomics identified glutamate and glutamine as novel predictive markers for structural anomalies, their vital role was also confirmed in the validation cohort with great predictive ability, and the area under the receiver operating characteristic curves (AUCs) were 0.862 and 0.894 respectively. And AUCs for glutamine/glutamate were 0.913 and 0.903 among the two cohorts., Conclusions: Our results suggested that the aberrant glutamine/glutamate metabolism in AF is associated with nonchromosomal modificantions fetal structural anomalies. Based on our findings, a novel screening method could be established for the nonchromosomal modificantions fetal structural anomalies. And the results also indicate that monitoring fetal metabolic conditions (especially glutamine and glutamine metabolism) may be helpful for antenatal diagnosis and therapy., Competing Interests: ZW and PY are co-founders of iphenome Yun Pu Kang biotechnology Inc. Author ZW is employed by PY. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest, (Copyright © 2023 Yuan, Liu, Wang, Huang, Liu, Huang, Wu, Liu, Yin and Yang.)

Whether and how certain transposable elements with viral origins, such as endogenous retroviruses (ERVs) dormant in our genomes, can become awakened and contribute to the aging process is largely unknown. In human senescent cells, we found that HERVK (HML-2), the most recently integrated human ERVs, are unlocked to transcribe viral genes and produce retrovirus-like particles (RVLPs). These HERVK RVLPs constitute a transmissible message to elicit senescence phenotypes in young cells, which can be blocked by neutralizing antibodies. The activation of ERVs was also observed in organs of aged primates and mice as well as in human tissues and serum from the elderly. Their repression alleviates cellular senescence and tissue degeneration and, to some extent, organismal aging. These findings indicate that the resurrection of ERVs is a hallmark and driving force of cellular senescence and tissue aging., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2022 The Author(s). Published by Elsevier Inc. All rights reserved.)

Cell membrane-coated nanoparticles are emerging as a new type of promising nanomaterials for immune evasion and targeted delivery. An underlying premise is that the unique biological functions of natural cell membranes can be conferred on the inherent physiochemical properties of nanoparticles by coating them with a cell membrane. However, the extent to which the membrane protein properties are preserved on these nanoparticles and the consequent bio-nano interactions are largely unexplored. Here, we synthesized two mesenchymal stem cell (MSC) membrane-coated silica nanoparticles (MCSNs), which have similar sizes but distinctly different stiffness values (MPa and GPa). Unexpectedly, a much lower macrophage uptake, but much higher cancer cell uptake, was found with the soft MCSNs compared with the stiff MCSNs. Intriguingly, we discovered that the soft MCSNs enabled the forming of a more protein-rich membrane coating and that coating had a high content of the MSC chemokine CXCR4 and MSC surface marker CD90. This led to the soft MCSNs enhancing cancer cell uptake mediated by the CD90/integrin receptor-mediated pathway and CXCR4/SDF-1 pathways. These findings provide a major step forward in our fundamental understanding of how the combination of nanoparticle elasticity and membrane coating may be used to facilitate bio-nano interactions and pave the way forward in the development of more effective cancer nanomedicines.

Gastric cancer (GC) is a common lethal malignancy worldwide. Gastroscopy is an effective screening technique for decreasing mortality. However, there are still limited useful non-invasive markers for early detection of GC. Bile acids are important molecules for the modulation of energy metabolism. With an in-depth targeted method for accurate quantitation of 80 bile acids (BAs), we aimed to find potential biomarkers for the early screening of GC. A cohort with 280 participants was enrolled, including 113 GC, 22 benign gastric lesions (BGL) and 145 healthy controls. Potential markers were identified using a random forest machine algorithm in the discovery cohort (n=180), then validated in an internal validation cohort (n=78) and a group with 22 BGL. The results represented significant alterations in the circulating BA pool between GC and the controls. BAs also exhibited significant correlations with various clinical traits. Then, we developed a diagnostic panel that comprised six BAs or ratios for GC detection. The panel showed high accuracy for the diagnosis of GC with AUC of 1 (95%CI: 1.00-1.00) and 0.98 (95%CI: 0.93-1.00) in the discovery and validation cohort, respectively. This 6-BAs panel was also able to identify early GC with AUC of 1 (95%CI: 0.999-1.00) and 0.94 (95%CI: 0.83-1.00) in the discovery and validation cohort, respectively. Meanwhile, this panel achieved a good differential diagnosis between GC and BGL and the AUC was 0.873 (95%CI: 0.812-0.934). The alternations of serum bile acids are characteristic metabolic features of GC. Bile acids could be promising biomarkers for the early diagnosis of GC., Competing Interests: ZW and PY are co-founders of iPhenome Yun Pu Kang Biotechnology Inc. ZW is an employee of iPhenome Yun Pu Kang Biotechnology Inc. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Pan, Deng, Wei, Wu, Zhang, Yuan, Liang, Liu and Yin.)

Pancreatic cancer (PC) is burdened with a low 5-year survival rate and high mortality due to a severe lack of early diagnosis methods and slow progress in treatment options. To improve clinical diagnosis and enhance the treatment effects, we applied metabolomics using ultra-high-performance liquid chromatography with a high-resolution mass spectrometer (UHPLC-HRMS) to identify and validate metabolite biomarkers from paired tissue samples of PC patients. Results showed that the metabolic reprogramming of PC mainly featured enhanced amino acid metabolism and inhibited sphingolipid metabolism, which satisfied the energy and biomass requirements for tumorigenesis and progression. The altered metabolism results were confirmed by the significantly changed gene expressions in PC tissues from an online database. A metabolites biomarker panel (six metabolites) was identified for the differential diagnosis between PC tumors and normal pancreatic tissues. The panel biomarker distinguished tumors from normal pancreatic tissues in the discovery group with an area under the curve (AUC) of 1.0 (95%CI, 1.000-1.000). The biomarker panel cutoff was 0.776. In the validation group, an AUC of 0.9000 (95%CI = 0.782-1.000) using the same cutoff, successfully validated the biomarker signature. Moreover, this metabolites panel biomarker had a great capability to predict the overall survival (OS) of PC. Taken together, this metabolomics method identifies and validates metabolite biomarkers that can diagnose the onsite progression and prognosis of PC precisely and sensitively in a clinical setting. It may also help clinicians choose proper therapeutic interventions for different PC patients and improve the survival of PC patients., Competing Interests: ZW and PY are co-founders of iPhenome (Yun Pu Kang) Biotechnology Inc. ZW is an employee of iPhenome (Yun Pu Kang) Biotechnology Inc. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Liu, Qin, Liu, Wei, Wu, Shang, Liu, Wang, Liu, Shang and Yin.)

A material system enabling specific NIR-II fluorescence imaging of Gram-positive bacteria is described. The material system is based on the electrostatic binding of Cu 2- x Se and vancomycin-modified NaGdF 4 :Nd,Yb@NaGdF 4 downconversion nanoparticles (DCNPs), the fluorescence of which is weak owing to the spectral overlap of Cu 2- x Se absorption with the DCNP NIR emission. The presence of Gram-positive bacteria precisely disconnects the bond between vancomycin-modified DCNPs and Cu 2- x Se, thus enabling a strong fluorescent signal. In vivo studies show that the material system can be specifically activated at the site of Gram-positive bacterial infection but is essentially nonfluorescent in the area of Gram-negative bacterial infection.

Background: Currently available prognostic tools and focused therapeutic methods result in unsatisfactory treatment of gastric cancer (GC). A deeper understanding of human epidermal growth factor receptor 2 (HER2)-coexpressed metabolic pathways may offer novel insights into tumour-intrinsic precision medicine., Methods: The integrated multi-omics strategies (including transcriptomics, proteomics and metabolomics) were applied to develop a novel metabolic classifier for gastric cancer. We integrated TCGA-STAD cohort (375 GC samples and 56753 genes) and TCPA-STAD cohort (392 GC samples and 218 proteins), and rated them as transcriptomics and proteomics data, resepectively. 224 matched blood samples of GC patients and healthy individuals were collected to carry out untargeted metabolomics analysis., Results: In this study, pan-cancer analysis highlighted the crucial role of ERBB2 in the immune microenvironment and metabolic remodelling. In addition, the metabolic landscape of GC indicated that alanine, aspartate and glutamate (AAG) metabolism was significantly associated with the prevalence and progression of GC. Weighted metabolite correlation network analysis revealed that glycolysis/gluconeogenesis (GG) and AAG metabolism served as HER2-coexpressed metabolic pathways. Consensus clustering was used to stratify patients with GC into four subtypes with different metabolic characteristics (i.e. quiescent, GG, AAG and mixed subtypes). The GG subtype was characterised by a lower level of ERBB2 expression, a higher proportion of the inflammatory phenotype and the worst prognosis. However, contradictory features were found in the mixed subtype with the best prognosis. The GG and mixed subtypes were found to be highly sensitive to chemotherapy, whereas the quiescent and AAG subtypes were more likely to benefit from immunotherapy., Conclusions: Transcriptomic and proteomic analyses highlighted the close association of HER-2 level with the immune status and metabolic features of patients with GC. Metabolomics analysis highlighted the co-expressed relationship between alanine, aspartate and glutamate and glycolysis/gluconeogenesis metabolisms and HER2 level in GC. The novel integrated multi-omics strategy used in this study may facilitate the development of a more tailored approach to GC therapy., Competing Interests: ZW and PY are co-founders of iphenome (Yun Pu Kang) biotechnology Inc. ZW is an employee of iphenome (Yun Pu Kang) biotechnology Inc. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Yuan, Deng, Pan, Ren, Wei, Wu, Zhang, Li, Yin and Shang.)

Bacterial diseases pose a serious threat to human health. Continued development of precise diagnostic methods and synergistic therapy techniques for combating bacteria are needed. Herein a hybrid nanosystem (Ag 2 S@ZIF-Van NS) was constructed by one-step self-assembly of Zn 2+ , vancomycin (Van) and Ag 2 S quantum dots (QDs). The nanosystem possesses excellent second near-infrared transparency window (NIR-II) fluorescence properties (∼1200 nm emission wavelength), good photothermal conversion properties, and biocompatibility. The material system enables precise, targeted NIR-II fluorescent imaging of bacterial inflammation in vivo as well as promoting anti-bacterial and wound healing effects.

Nuclear deformation, a hallmark frequently observed in senescent cells, is presumed to be associated with the erosion of chromatin organization at the nuclear periphery. However, how such gradual changes in higher-order genome organization impinge on local epigenetic modifications to drive cellular mechanisms of aging has remained enigmatic. Here, through large-scale epigenomic analyses of isogenic young, senescent, and progeroid human mesenchymal progenitor cells (hMPCs), we delineate a hierarchy of integrated structural state changes that manifest as heterochromatin loss in repressive compartments, euchromatin weakening in active compartments, switching in interfacing topological compartments, and increasing epigenetic entropy. We found that the epigenetic de-repression unlocks the expression of pregnancy-specific beta-1 glycoprotein (PSG) genes that exacerbate hMPC aging and serve as potential aging biomarkers. Our analyses provide a rich resource for uncovering the principles of epigenomic landscape organization and its changes in cellular aging and for identifying aging drivers and intervention targets with a genome-topology-based mechanism., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2022 Elsevier Inc. All rights reserved.)

To investigate the exposure of infants to phenylpyrazole and diamide insecticides during lactation, we collected 3467 breast milk samples of lactating women from 100 cities of 24 provinces in China and prepared 100 pooled samples together city-by-city. Among phenylpyrazole insecticides, fipronil and its metabolites (63-100%) were widely detected in breast milk, with total detection concentrations ranging from 178 to 2947 ng/L (median: 921 ng/L). Among diamide insecticides, chlorantraniliprole and flubendiamide were detected in breast milk, but their detection frequencies (20-85%) and concentration levels (nondetected to 89.9 ng/L) were far lower than those of total fipronils. The average estimated daily intake of infants exposed to total fipronils through breast milk is 209 ng/kg-bw/day by upper-bound scenario evaluation, which is higher than the acceptable daily intake (200 ng/kg-bw/day). This study indicates that infants have far higher exposure levels to fipronil than adults, while exposure levels to other types of phenylpyrazoles and diamide insecticides are low.

Aging in humans is intricately linked with alterations in circadian rhythms concomitant with physiological decline and stem cell exhaustion. However, whether the circadian machinery directly regulates stem cell aging, especially in primates, remains poorly understood. In this study, we found that deficiency of BMAL1, the only non-redundant circadian clock component, results in an accelerated aging phenotype in both human and cynomolgus monkey mesenchymal progenitor cells (MPCs). Unexpectedly, this phenotype was mainly attributed to a transcription-independent role of BMAL1 in stabilizing heterochromatin and thus preventing activation of the LINE1-cGAS-STING pathway. In senescent primate MPCs, we observed decreased capacity of BMAL1 to bind to LINE1 and synergistic activation of LINE1 expression. Likewise, in the skin and muscle tissues from the BMAL1-deficient cynomolgus monkey, we observed destabilized heterochromatin and aberrant LINE1 transcription. Altogether, these findings uncovered a noncanonical role of BMAL1 in stabilizing heterochromatin to inactivate LINE1 that drives aging in primate cells., (© The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Apolipoprotein E (APOE) is a component of lipoprotein particles that function in the homeostasis of cholesterol and other lipids. Although APOE is genetically associated with human longevity and Alzheimer's disease, its mechanistic role in aging is largely unknown. Here, we used human genetic, stress-induced and physiological cellular aging models to explore APOE-driven processes in stem cell homeostasis and aging. We report that in aged human mesenchymal progenitor cells (MPCs), APOE accumulation is a driver for cellular senescence. By contrast, CRISPR-Cas9-mediated deletion of APOE endows human MPCs with resistance to cellular senescence. Mechanistically, we discovered that APOE functions as a destabilizer for heterochromatin. Specifically, increased APOE leads to the degradation of nuclear lamina proteins and a heterochromatin-associated protein KRAB-associated protein 1 via the autophagy-lysosomal pathway, thereby disrupting heterochromatin and causing senescence. Altogether, our findings uncover a role of APOE as an epigenetic mediator of senescence and provide potential targets to ameliorate aging-related diseases., (© 2022. The Author(s), under exclusive licence to Springer Nature America, Inc.)

On the basis of ensuring the quality and concealment of steganographic images, this paper proposes a double-matrix decomposition image steganography scheme with multi-region coverage, to solve the problem of poor extraction ability of steganographic images under attack or interference. First of all, the cover image is transformed by multi-wavelet transform, and the hidden region covering multiple wavelet sub-bands is selected in the wavelet domain of the cover image to embed the secret information. After determining the hidden region, the hidden region is processed by Arnold transform, Hessenberg decomposition, and singular-value decomposition. Finally, the secret information is embedded into the cover image by embedding intensity factor. In order to ensure robustness, the hidden region selected in the wavelet domain is used as the input of Hessenberg matrix decomposition, and the robustness of the algorithm is further enhanced by Hessenberg matrix decomposition and singular-value decomposition. Experimental results show that the proposed method has excellent performance in concealment and quality of extracted secret images, and secret information is extracted from steganographic images attacked by various image processing attacks, which proves that the proposed method has good anti-attack ability under different attacks.

Regenerative capacity declines throughout evolution and with age. In this study, we asked whether metabolic programs underlying regenerative capability might be conserved across species, and if so, whether such metabolic drivers might be harnessed to promote tissue repair. To this end, we conducted metabolomic analyses in two vertebrate organ regeneration models: the axolotl limb blastema and antler stem cells. To further reveal why young individuals have higher regenerative capacity than the elderly, we also constructed metabolic profiles for primate juvenile and aged tissues, as well as young and aged human stem cells. In joint analyses, we uncovered that active pyrimidine metabolism and fatty acid metabolism correlated with higher regenerative capacity. Furthermore, we identified a set of regeneration-related metabolite effectors conserved across species. One such metabolite is uridine, a pyrimidine nucleoside, which can rejuvenate aged human stem cells and promote regeneration of various tissues in vivo. These observations will open new avenues for metabolic intervention in tissue repair and regeneration., (© 2022. The Author(s).)

In response to the problems of high complexity and the large amount of operations of existing color image encryption algorithms, a low-complexity, low-operation color image encryption algorithm based on a combination of bit-plane and chaotic systems is proposed that is interrelated with plaintext information. Firstly, three channels of an RGB image are extracted, and the gray value of each pixel channel can be expressed by an eight-bit binary number. The higher- and lower-four bits of the binary gray value of each pixel are exchanged, and the position of each four-bit binary number is scrambled by a logistic chaotic sequence, and all the four-bit binary numbers are converted into hexadecimal numbers to reduce the computational complexity. Next, the position of the transformed image is scrambled by a logistic chaotic sequence. Then, the Chen chaos sequence is used to permute the gray pixel values of the permuted image. Finally, the gray value of the encrypted image is converted into a decimal number to form a single-channel encrypted image, and the three-channel encrypted image is synthesized into an encrypted color image. Through MATLAB simulation experiments, a security analysis of encryption effects in terms of a histogram, correlation, a differential attack, and information entropy is performed. The results show that the algorithm has a better encryption effect and is resistant to differential attacks.

Background and Aims: The diagnosis of Wilson's disease (WD) is challenging by clinical or genetic criteria. A typical early pathological change of WD is the increased liver lipid deposition and lowered serum triglyceride (TG). Therefore, the contents of serum lipids may provide evidence for screening of biomarkers for WD. Methods: 34 WD patients, 31 WD relatives, and 65 normal controls were enrolled in this study. Serum lipidomics data was acquired by an ultra-high-performance liquid chromatography high-resolution mass spectrometry system, and the data were analyzed by multivariate statistical methods. Results: Of all 510 identified lipids, there are 297 differential lipids between the WD and controls, 378 differential lipids between the relatives and controls, and 119 differential lipids between the patients and relatives. In WD, the abundances of most saturated TG were increased, whereas other unsaturated lipids decreased, including phosphatidylcholine (PC), sphingomyelin (SM), lysophosphatidylcholine (LPC), ceramide (Cer), and phosphatidylserine (PS). We also found many serum lipid species may be used as biomarkers for WD. The areas under the receiver operating characteristic curve (AUC) of PS (35:0), PS (38:5), and PS (34:0) were 0.919, 0.843, and 0.907. The AUCs of TG (38:0) and CerG1 (d42:2) were 0.948 and 0.915 and the AUCs of LPC (17:0) and LPC (15:0) were 0.980 and 0.960, respectively. The lipid biomarker panel exhibits good diagnostic performance for WD. The correlation networks were built among the different groups and the potential mechanisms of differential lipids were discussed. Interestingly, similar lipid profile of WD is also found in their relatives, which indicated the changes may also related to the mutation of the ATP7B gene. Conclusions: Lipid deregulation is another important hallmark of WD besides the deposition of copper. Our lipidomic results provide new insights into the diagnostic and therapeutic targets of WD., Competing Interests: Author ZW is employed by iPhnome (Yun Pu Kang) biotechnology Inc. Dalian. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Zhi, Sun, Jiao, Pan, Wu, Liu, Su, Zhou, Shang, Niu, Hua and Yin.)

To address the problems of the high complexity and low security of the existing image encryption algorithms, this paper proposes a dynamic key chaotic image encryption algorithm with low complexity and high security associated with plaintext. Firstly, the RGB components of the color image are read, and the RGB components are normalized to obtain the key that is closely related to the plaintext, and then the Arnold transform is used to stretch and fold the RGB components of the color image to change the position of the pixel points in space, so as to destroy the correlation between the adjacent pixel points of the image. Next, the generated sequences are independently encrypted with the Arnold-transformed RGB matrix. Finally, the three encrypted images are combined to obtain the final encrypted image. Since the key acquisition of this encryption algorithm is related to the plaintext, it is possible to achieve one key per image, so the key acquisition is dynamic. This encryption algorithm introduces chaotic mapping, so that the key space size is 10180. The key acquisition is closely related to the plaintext, which makes the ciphertext more random and resistant to differential attacks, and ensures that the ciphertext is more secure after encryption. The experiments show that the algorithm can encrypt the image effectively and can resist attack on the encrypted image.

Nanoparticles in intercellular gaps, junctions, or seals could have close contact with neighboring cells simultaneously. Understanding the interaction between intercellular nanoparticles and confining cell membranes is of fundamental importance, not only to the unravelling of endocytic mechanisms but also to implications such as controlled drug delivery in tumor tissues. Here we theoretically examine the mechanical behaviors of adhesive cylindrical nanoparticles confined between two lipid membrane patches of finite size. As the size of the particle-membrane contact region or wrapping degree increases, neighboring cylindrical nanoparticles become separated and the nanoparticle distance increases first and then decreases until the particles are fully trapped by adjacent membrane patches. Depending on the nanoparticle size, adhesion energy, membrane bending rigidity and tension, and intermembrane distance, three characteristic particle-membrane interaction phases are determined as no wrapping, partial trapping, and full trapping, and the corresponding interaction phase diagram is established. Further energy comparison indicates that multiple nanoparticles undergoing the two-membrane trapping process do not exhibit cooperative effects. Analytical estimations on the system energy and configurations at equilibrium are performed based on the force balance of the membranes at small deformation and match well with numerical solutions. The results shed light on the mechanical behaviors of multiple nanoparticles in cell junctions or gaps and may have implications for drug delivery in tumor tissues.

Osteoporosis is becoming a highly prevalent disease in a large proportion of the global aged population. Serum metabolite markers may be important for the treatment and early prevention of osteoporosis. Serum samples from 32 osteoporosis and 32 controls were analyzed by untargeted metabolomics and lipidomic approaches performed on an ultra-high performance liquid chromatography and high-resolution mass spectrometry (UHPLC-HRMS) system. To find systemic disturbance of osteoporosis, weighted gene correlation network analysis (WGCNA) and statistical methods were employed for data-mining. Then, an in-depth targeted method was utilized to determine potential markers from the family of key metabolites. As a result, 1,241 metabolites were identified from untargeted methods and WGCNA indicated that lipids metabolism is deregulated and glycerol phospholipids, sphingolipids, fatty acids, and bile acids (BA) are majorly affected. As key metabolites of lipids metabolism, 66 bile acids were scanned and 49 compounds were quantified by a targeted method. Interestingly, hyocholic acids (HCA) were found to play essential roles during the occurrence of osteoporosis and may be potential markers. These metabolites may be new therapeutic or diagnosis targets for the screening or treatment of osteoporosis. Quantified measurement of potential markers also enables the establishment of diagnostic models for the following translational research in the clinic., Competing Interests: Author ZW was employed by the company iPhenome biotechnology (Yun Pu Kang) Inc. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Deng, Pan, Wu, Sun, Liu, Xiang, Yin and Shang.)

Sirtuin 3 (SIRT3) is an NAD+-dependent deacetylase linked to a broad range of physiological and pathological processes, including aging and aging-related diseases. However, the role of SIRT3 in regulating human stem cell homeostasis remains unclear. Here we found that SIRT3 expression was downregulated in senescent human mesenchymal stem cells (hMSCs). CRISPR/Cas9-mediated depletion of SIRT3 led to compromised nuclear integrity, loss of heterochromatin and accelerated senescence in hMSCs. Further analysis indicated that SIRT3 interacted with nuclear envelope proteins and heterochromatin-associated proteins. SIRT3 deficiency resulted in the detachment of genomic lamina-associated domains (LADs) from the nuclear lamina, increased chromatin accessibility and aberrant repetitive sequence transcription. The re-introduction of SIRT3 rescued the disorganized heterochromatin and the senescence phenotypes. Taken together, our study reveals a novel role for SIRT3 in stabilizing heterochromatin and counteracting hMSC senescence, providing new potential therapeutic targets to ameliorate aging-related diseases., (© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.)