Search Results (218)

Human ageing and longevity are increasingly understood as biologically integrated and heterogeneous processes shaped by interactions among genetic susceptibility, epigenetic remodelling, and environmental modulation. This narrative review examines these interconnections within a nutrigenomic framework, with particular emphasis on how inherited variation and epigenetic plasticity may influence responses to ageing-related interventions. A structured literature search was conducted in PubMed, Scopus, Web of Science, and Embase, focusing on English-language studies published during the last 10 years. The review was organized into three major domains: (i) genetic determinants of longevity, (ii) epigenetic mechanisms of ageing, and (iii) intervention-responsive pathways relevant to precision geroscience. Current evidence supports a polygenic model of longevity in which loci such as FOXO3 and APOE show the most consistent human associations, while telomere maintenance, insulin/IGF-1 and mTOR signalling, sirtuins, Klotho, inflammatory mediators, and DNA repair remain biologically important but variably supported at the variant level. Epigenetic mechanisms, including DNA methylation drift, epigenetic clocks, histone modifications, chromatin remodelling, heterochromatin loss, and non-coding RNA regulation, provide an environmentally responsive interface linking genetic background to ageing phenotypes. Nutritional, pharmacological, behavioural, and circadian interventions converge on overlapping molecular pathways involving AMPK, mTOR, FOXO, sirtuins, autophagy, mitochondrial maintenance, and inflammatory signalling, although human evidence remains heterogeneous and biomarker modulation should not be equated with clinically meaningful slowing of organismal ageing. Overall, this review highlights the value of integrating genetics, epigenetics, and intervention biology to support a more cautious and translationally relevant model of healthy ageing. It also underscores the need for precision nutrigeroscience approaches that account for tissue context, baseline physiology, and inter-individual molecular variability. Full article

Over the past two decades, numerous studies have examined the etiological significance of DNA fragmentation in human sperm using methods such as the comet assay (CA), the sperm chromatin structure assay, the sperm chromatin dispersion assay, and the TUNEL assay. We developed single-cell pulsed-field gel electrophoresis techniques, including one-dimensional (1D-SCPFGE) and angle-modulated two-dimensional (2D-SCPFGE), to detect early signs of naturally occurring DNA fragmentation. Comparative studies using purified human sperm with and without DNA fragmentation revealed some technical limitations in the conventional methods. This technical review outlines the procedures to ensure the quantitative performance of SCPFGE: (1) The mass of naked DNA was prepared through simultaneous in-gel swelling and proteolysis, which are highly sensitive to chemical and physical factors. Notably, these processes are vulnerable to reactive oxygen species (ROS). We developed the anti-ROS SCPFGE system to prevent artifactual cleavages. (2) 1D-SCPFGE discharges long-chain fibers from the origin, separating fibrous and granular segments beyond the tips of the fibers. (3) During continuous electrophoresis after 150° rotation (2D-SCPFGE-0-150), long-chain fibers unexpectedly extended diagonally backward from the origin, with long fibrous segments pulled out from a bundle that extended during the first electrophoresis, indicating some fibrous segments were embedded within the long-chain fibers. Even when SCPFGE was employed, one-directional current led to false negatives. (4) 2D-SCPFGE with angle rotation is currently the most sensitive imaging method for single-nuclear DNA fibers. However, without knowing the size of DNA fragments, it remains a semi-quantitative analysis. (5) To prevent artifactual DNA cleavage caused by ice crystals, low-temperature liquid storage is recommended. (6) The in-gel proteolyzed naked DNA is suitable as a substrate for chemical and enzymatic DNA cleavage analyses. Full article

Cellular senescence (CSEN) is caused by a variety of factors that trigger complex molecular pathways. These include telomere shortening, oncogene activation and replicative stress, as well as DNA damage caused by genotoxic anticancer drugs and endogenous and exogenous genotoxins. Here, we review the induction of CSEN by exogenous genotoxic insults resulting from food and environmental exposures. The available data show that genotoxins/carcinogens in tobacco smoke and smokeless tobacco, in the environment, in food, beverages and life-style products induce CNS. The exposures include N-nitroso compounds, polycyclic aromatic hydrocarbons, heterocyclic aromatic amines, acrylamide, heavy metals, fine dust, mycotoxins, phytotoxins, and phycotoxins. Also, heme in red meat contributes to CSEN as it catalyzes the formation of genotoxic species in the colon. Induction of CSEN by external genotoxins/carcinogens is bound on the DNA damage response pathway (DDR), which relies on activation of the ATM/ATR-CHK2/CHK1-p53-p21 axis and the p53-independent p16/p14 axis, eliciting cyclin-dependent kinase inhibition and permanent cell cycle arrest. Other factors that can be involved are DREAM, MAPK, cGAS/Sting, and NF-κB. The accumulation of non-repaired DNA damage triggering CSEN following external genotoxic exposures may contribute significantly to the amelioration of senescent cells and organ failure with age in humans. Senescent cells drive, via the senescence-associated secretory phenotype (SASP), inflammation that is involved in many diseases, including cancer. Although most of the studies were performed with in vitro cell systems, the consequences of CSEN induction by genotoxic nutritional components and environmental exposures seem to be underestimated. Since CSEN correlates with aging, it is reasonable to conclude that exogenous genotoxic pollutants contribute significantly to the aging process through CSEN induction. In light of these findings, it is deduced that reducing genotoxin exposures and using “rejuvenation” supplements (senotherapeutics) are reasonable strategies to counteract cellular senescence and the aging process. Full article

Background: Advanced paternal age is increasingly encountered in assisted reproduction as parenthood is deferred. The clinical question is whether paternal age from about 40 to 45 years and older affects embryo development or outcomes, and to what extent any effect relates to the sperm epigenome. Methods: This narrative review synthesized PubMed-indexed evidence on sperm aging biology, including DNA methylation, chromatin packaging and nucleosome retention, small non-coding RNAs, telomere dynamics, DNA fragmentation, and oxidative and mitochondrial stress, and their potential clinical impact on assisted reproduction outcomes. Results: Maternal age remains the principal determinant of embryo aneuploidy. After multivariable adjustment, independent paternal-age effects on fertilization, blastocyst formation, and preimplantation genetic testing for aneuploidy are small or not detected. At very advanced paternal ages near or above 50 years, some studies report higher miscarriage and lower live birth, without a consistent change in early embryo morphology. Aging in men is linked to higher DNA fragmentation and oxidative and mitochondrial signatures, together with reproducible sperm-epigenome changes, including age-linked DNA methylation, altered histone retention, and small-RNA shifts. These molecular findings support modest intergenerational influences on early development, while stable transgenerational inheritance in humans is not supported. Conclusions: Advanced paternal age should be regarded as a risk modifier rather than a primary driver of preimplantation failure. Counseling should emphasize realistic effect sizes and the predominance of maternal age. Laboratory workflows should minimize oxidative stress. Selective DNA-fragmentation testing may be appropriate in recurrent ART failure or recurrent loss. Sperm-epigenome assays remain investigational and should undergo prospective, standardized validation before use in routine care. Full article

Chronic ultraviolet (UV) exposure disrupts dermal collagen homeostasis and accelerates skin aging. This study evaluated the protective effects of black ginseng extract (BGE) against UV-induced photoaging in human dermal fibroblasts. BGE restored collagen-related markers, including COL5A1 and COL7A1, improved fibroblast proliferative capacity, and reduced senescence-associated changes under UV stress. Data-independent acquisition (DIA) proteomics identified broad pathway modulation by BGE, involving extracellular matrix remodeling, chromatin organization, and stress-response processes. To validate genome maintenance-related signals highlighted by proteomics, qPCR showed that BGE increased telomere/replication-associated genes compared with the UV group, including POT1 (2.29-fold) and ORC1 (6.70-fold). In addition, comet assay imaging indicated reduced UV-associated DNA damage features following BGE treatment. Overall, these findings indicate that BGE mitigates UV-induced photoaging phenotypes in fibroblasts, with collagen-related recovery and multi-level protective responses, supporting its potential as a natural bioactive ingredient for anti-photoaging skincare applications. Full article

Telomere length is a crucial marker of cellular aging and genomic stability, with significant implications for age-related diseases and cancers. This study introduces an improved quantitative PCR (qPCR) method for measuring absolute telomere length, addressing the need for accurate and high-throughput assessment in both clinical and research settings. Novel primers were designed for the single-copy gene interferon beta (IFNB1) to serve as an internal control, alongside a series of single-stranded oligonucleotide standards to establish a calibration curve. This approach allows for precise quantification of telomere length in kilobases per single copy gene copy number per chromosome. We validated this method using DNA samples from peripheral blood and buccal swabs from 17 healthy human volunteers, as well as umbilical cord blood from 9 healthy newborn babies, demonstrating its high linearity and reproducibility. Our findings indicate that this improved qPCR technique provides a rapid, cost-effective, and accurate means of measuring absolute telomere length, thereby facilitating large-scale studies and enhancing clinical diagnostics related to telomere biology. Full article

Background: Outcomes after critical illness vary markedly despite similar diagnoses and severity scores, underscoring the limitations of chronological age and conventional Intensive Care Unit (ICU) prognostic tools. Personalization of critical care is increasingly essential to improve not only short-term survival but also long-term post-discharge outcomes. Biological aging clocks provide a quantitative framework to capture physiological reserve, immune competence, and vulnerability to stress. Methods: We conducted a scoping review of original human studies published between January 2015 and October 2025 that evaluated biological aging biomarkers in adult ICU populations. PubMed/MEDLINE, Scopus, Web of Science, and Embase were searched, with backward citation screening. Results: Across epigenetic, telomere-based, cfDNA, proteomic, metabolomic, and phenotypic aging measures, accelerated biological aging was consistently associated with increased mortality, organ dysfunction, and post-ICU vulnerability. Despite substantial methodological heterogeneity, a convergent signal emerged linking inflammation-weighted and stress-responsive deep biological clocks to clinically meaningful outcomes in critically ill patients. Conclusions: Biological aging biomarkers represent a mechanistically grounded approach to personalized prognostication in critical care. From a translational perspective, deep biological clocks hold promise for personalized risk stratification, prognostication, and the identification of high-risk recovery phenotypes, although prospective validation and implementation studies are required. Full article

Background/Objectives: Segmental duplications (SDs) are major drivers of genome evolution and structural variation in primates, particularly within acrocentric chromosomes, where rDNA arrays and duplicated sequences are densely clustered. However, the evolutionary dynamics of rDNA-linked SDs across great ape lineages have remained poorly characterized due to longstanding technical limitations in genome assembly. Here, we investigate the organization, copy number variation, and evolutionary conservation of acrocentric SDs in great apes by integrating fluorescence in situ hybridization (FISH) with comparative analyses of telomere-to-telomere (T2T) genome assemblies. Methods: Using eight human-derived fosmid probes targeting SD-enriched regions flanking rDNA arrays, we analyzed multiple individuals from chimpanzee, bonobo, gorilla, and both Bornean and Sumatran orangutans. Results: Our FISH analyses revealed extensive lineage-specific variation in SD copy number and chromosomal distribution, with pronounced heteromorphism in African great apes, particularly gorillas, and more conserved patterns in orangutans. Several SDs showed fixed duplications across species, while others exhibited high levels of polymorphism and individual-specific organization. Conclusions: Comparison with T2T assemblies confirmed consistent genomic localization for a subset of probes, whereas others displayed partial discordance, highlighting the persistent challenges in resolving highly repetitive and structurally dynamic regions even with state-of-the-art assemblies. Genome-wide analyses further revealed species-specific enrichment of SDs on rDNA-bearing chromosomes, with chimpanzees and bonobos showing higher proportions than gorillas, and contrasting patterns between the two orangutan species. Overall, our results demonstrate that rDNA-linked SDs represent highly dynamic genomic compartments that have undergone differential expansion and remodeling during great ape evolution. These regions contribute substantially to inter- and intra-species structural variation and provide a mechanistic substrate for lineage-specific genome evolution, underscoring the importance of integrating cytogenetic and T2T-based approaches to fully capture the complexity of duplicated genomic landscapes. Full article

The reduction in oocyte competence and ovarian reserve coincides with reproductive ageing; nevertheless, the molecular mechanisms underlying this phenomenon remain poorly understood. Our testable mechanistic hypothesis is that the oxidative stress–telomere axis is a crucial regulatory mechanism controlling meiotic stability, mitochondrial resilience, and granulosa cell integrity. This notion posits that granulosa and cumulus cells have accelerated telomere attrition and impaired DNA-damage responses due to elevated amounts of reactive oxygen species, which also induce oxidative guanine lesions, inhibit telomerase function, and generate telomeric replication stress. This telomere-dependent vulnerability is anticipated to compromise developmental competence, disrupt meiotic spindle integrity, and diminish metabolic support to the oocyte, prior to observable declines in AMH or follicle count. Data from human IVF cohorts supports the model: Conditions such as PCOS, endometriosis, and POI have unique oxidative-telomeric profiles, whereas diminished telomere length in granulosa cells, reduced telomerase activity, and worse fertilisation, blastulation, and pregnancy outcomes are associated with increased follicular oxidative DNA damage. The findings suggest that oxidative DNA damage (8-OHdG), telomerase activity, and the structure of granulosa-cell telomeres may serve as preliminary indicators of preclinical ovarian ageing. This theory may be directly evaluated in forthcoming longitudinal studies and specific treatments related to telomerase regulation, mitochondrial medicines, or redox modulation. Consequently, the oxidative stress–telomere axis may represent a vital physiologic factor affecting reproductive lifespan and a prospective target for personalised ART techniques. Full article

The pathogenesis of koala retrovirus (KoRV) has been explored in various contexts, yet its role in tumorigenesis remains incompletely understood. Unlike acute transforming retroviruses, KoRV lacks a viral oncogene but may contribute to oncogenesis via indirect mechanisms. However, the relationship between KoRV and telomere length, as a potential indicator of telomerase activity, has not been examined. This study investigates the effect of KoRV infection on telomere length in 47 samples from Southern Australian koalas in a novel telomere length quantification method. Telomere lengths of 30 KoRV-negative samples were compared to those of 17 KoRV-positive samples using the Absolute Human Telomere Length Quantification qPCR kit (ScienCell Research Laboratories, California, USA). The telomere length in KoRV-infected WBCs was significantly longer than the uninfected ones (t = −2.059, p-value = 0.045). In line with this, telomere length correlated positively with proviral load (r = 0.421, p-value = 0.003), further linking viral burden to telomere elongation. Furthermore, the effect of age on telomere length differed by infection status (β = −5329.7, p-value = 0.0038); KoRV-positive individuals exhibited longer telomeres at a younger age but experienced more rapid telomere attrition over time compared to KoRV-negative individuals. These results suggest KoRV promotes telomerase elongation ability and modulates age-related telomere dynamics, potentially contributing to subsequent cellular immortality and oncogenesis. These pathways may overlap with other retroviruses, where telomerase dysregulation contributes to their oncogenic potential. This study provides new insights into KoRV pathogenesis and DNA quantification methodology, which could be valuable for future research by identifying predictive markers for tumour progression and potential therapeutic targets in affected koalas. Full article

Recent advances in sequencing methods have led to major progress in the gapless assemblies of the human genome. However, until mid-2023, the complete sequence of the Y chromosome remained elusive. While only a small percentage of autosomal chromosomes were without complete sequences in the broadly used reference assembly of the human genome (GRCh38), around 50% of the chromosome Y DNA sequence was unknown. Using a sophisticated computational approach, we analyzed the presence of short inverted repeats in the current human reference genome (GRCh38) and in the Telomere-to-Telomere (T2T) assembly of chromosome Y. This analysis identified the location of the repeats in chromosome Y and highlighted their association with functionally annotated sequences. The comparison revealed notably more inverted repeats in the T2T assembly compared to GRCh38. These are located abundantly around exons and mobile elements, and, unexpectedly, also within gene annotations. The remarkable abundance of short inverted repeats around exons points to their importance in gene regulation, and their presence in regions associated with recombination suggests crucial roles in recombination processes. Interestingly, the most underestimated sequences in the T2T assembly are inverted repeats with a repeat length of 12–14, which are more than 20 times as frequent as those in the human reference genome GRCh38. These findings indicate that the number of short inverted repeats was significantly underestimated in the current human reference genome (GRCh38). These previously unidentified sites are of great bio-medicinal potential, as inverted repeats are precursors for the formation of cruciform DNA functional epitopes. Full article

Genomic instability markers are important hallmarks of aging, as previously evidenced within the European study of biomarkers of human aging, MARK-AGE; however, establishing the specific metabolic determinants of vascular aging is challenging. The objective of the present study was to evaluate the impact of the susceptibility to oxidation of serum LDL particles (LDLox) and the plasma metabolization products of nitric oxide (NOx) on relevant genomic instability markers. The analysis was performed on a MARK-AGE cohort of 1326 subjects (635 men and 691 women, 35–75 years old) randomly recruited from the general population. The Inverse Probability of Treatment Weighting causal inference algorithm was implemented in order to assess the potential causal relationship between the LDLox and NOx octile-based thresholds and three genomic instability markers measured in mononuclear leukocytes: the percentage of telomeres shorter than 3 kb, the initial DNA integrity, and the DNA damage after irradiation with 3.8 Gy. The results showed statistically significant telomere shortening for LDLox, while NOx yielded a significant impact on DNA integrity. Overall, the effect on the genomic instability markers was higher than for the confirmed vascular aging determinants, such as low HDL cholesterol levels, indicating a meaningful impact even for small changes in LDLox and NOx values. Full article

Background: Centromeric alpha satellite DNA is organized into higher-order repeats (HORs), whose precise structure is often difficult to resolve in standard genome assemblies. The recent telomere-to-telomere (T2T) assembly of the human genome enables complete analysis of centromeric regions, including the full structure of HOR arrays. Methods: We applied the novel high-precision GRMhor algorithm to the complete T2T-CHM13 assembly of human chromosome 21. GRMhor integrates global repeat map (GRM) and monomer distance (MD) diagrams to accurately identify, classify, and visualize HORs and their subfragments. Results: The analysis revealed a novel Cascading 11mer HOR array, in which each canonical HOR copy comprises 11 monomers belonging to 10 different monomer types. Subfragments with periodicities of 4, 7, 9, and 20 were identified within the array. A second, complex 23/25mer HOR array of mixed Willard’s/Cascading type was also detected. In contrast to the hg38 assembly, where a dominant 8mer and 33mer HOR were previously annotated, these structures were absent in the T2T-CHM13 assembly, highlighting the limitations of hg38. Notably, we discovered a novel 52mer HOR—the longest alpha satellite HOR unit reported in the human genome to date. Several subfragment repeats correspond to alphoid subfamilies previously identified using restriction enzyme digestion, but are here resolved with higher structural precision. Conclusions: Our findings demonstrate the power of GRMhor in resolving complex and previously undetected alpha satellite architectures, including the longest canonical HOR unit identified in the human genome. The precise delineation of superHORs, Cascading structures, and HOR subfragments provides unprecedented insight into the fine-scale organization of the centromeric region of chromosome 21. These results highlight both the inadequacy of earlier assemblies, such as hg38, and the critical importance of complete telomere-to-telomere assemblies for accurately characterizing centromeric DNA. Full article

The use of DNA as a scaffold for nanoclusters is particularly interesting due to its structural versatility and easy integration with aptamers. In their structure, aptamers often contain non-canonical forms of DNA, i.e., G-quadruplexes (GQs). Four-stranded GQs are used to construct nanomachines and biosensors for monitoring changes in the concentration of potassium ions. In the present study, we continue our work related to the synthesis of silver nanoclusters formed on a bifunctional DNA template. By attaching a cytosine-rich domain (C12) to a G-quadruplex-forming sequence—human telomeric (Tel22) or thrombin-binding aptamer (TBA)—we constructed bifunctional templates for fluorescent silver nanoclusters (C12) with the ability to detect potassium ions (GQs). The changing localization of the C12 domain from the 3′ to 5′ end of the oligonucleotide was a successful way to improve the fluorescence properties of the obtained fluorescent probes. The best performance as a probe for potassium ions was exhibited by C12Tel22-AgNCs, with an LOD of 0.68 mM in PBS. The introduction of the fluorescent cytosine analog tC leads to an LOD of 0.68 mM in PBS and 0.46 mM in Tris-acetate. Additionally, we performed AFM, TEM, DLS analysis, and cellular studies to further investigate the structural properties and behavior of the Tel22C12-AgNCs in biological contexts. Full article

Antiretroviral therapy (ART) has significantly improved the prognosis of human immunodeficiency virus type 1 (HIV-1) infection. Although ART can suppress plasma viremia below detectable levels, it cannot eradicate the HIV-1 DNA (provirus) integrated into the host cell genome. This integration often results in unrepaired DNA damage due to the HIV-1-induced inhibition of DNA repair pathways. Furthermore, HIV-1 infection causes telomere attrition in host chromosomes, a critical factor contributing to CD4+ T cell senescence and apoptosis. HIV-1 proteins can induce DNA damage, block DNA replication, and activate DNA damage responses across various organs. In this review, we explore multiple aspects of the intricate interactions between HIV-1 and the host genome involved in CD4+ T cell depletion, inflammaging, the clonal expansion of infected cells in long-term-treated patients, and viral latency. We discuss the molecular mechanisms of DNA damage that contribute to comorbidities in HIV-1-infected individuals and highlight emerging therapeutic strategies targeting the integrated HIV-1 provirus. Full article