Pregnancy loss is one of the most common adverse events during the first weeks of gestation, and the incidence increases with maternal age and in presence of selected risk factors. Nonetheless, no risk factors have been identified in most cases, considering these cases unexplained. Fertility rate decreases as maternal age increases and epigenetic age-dependent conditions may favor miscarriage. DNA methylation and telomere length are informative of aging and cell senescence, and their assessment has been evaluated as predictors of successful pregnancy. Telomere length (TL; T/S) and LINE-1 methylation (LINE-1;%) have been assessed in a cohort of 242 pregnant women by comparing spontaneous early miscarriage (EPL, n = 129) with voluntary interruption (VPI, n = 113). Telomere size and LINE-1 methylation rate drastically decreased as the age of women increased (P < 0.000001) with EPL group having lower values (T/S: 322.6 ± 142.0 versus 455.0 ± 290.6; P < 0.000001 and LINE-1%: 81.66 ± 4.2 versus 86.01 ± 3.7; P < 0.000001) also characterized by stronger age-dependent lowering compared to VPI (P = 0.00035 and P < 0.000001, respectively). A global improvement in TL was observed as LINE-1 methylation rate increased, and it was more evident in EPL than in VPI (P < 0.000001). Focusing on the area below the 25th percentile of TL and LINE-1% distribution, an overrepresentation of EPL cases was observed (P < 0.000001). On the contrary, VPI controls were dramatically overrepresented (P < 0.000001) in the area above the respective 75th percentiles. The mutual comparison of the number of EPL and VPI in these two extreme areas (EPL/VPI(<25th) = 3.12 versus EPL/VPI(>75th) = 0.32) yielded a significant risk of early pregnancy failure when women carried both risk conditions, low TL and LINE-1 methylation (OR = 9.70, 3.94-23.72; P < 0.0001). The intracase analyses ascribed to recurrent EPL cases even higher risks (OR = 10.5, 3.6-29.5; P < 0.0001) and a risk dosage effect stratification recognized to low methylation highest odds than that of short telomeres (OR = 4.44, 2.45-8.03; P < 0.0001 and OR = 2.26, 1.26-4.04; P = 0.005, respectively). Overall, this suggests a combined effect of short telomeres and low methylation in phenotype worsening and a significant role of methylation in sustaining telomere size. These data support the hypothesis that different levels of DNA methylation may capture different biological mechanisms underlying telomere dynamics and dysfunctions and chromatin organization. Therefore, the concomitant assessment of telomere, methylation and their mutual interactions may be a novel strategy to translate the classical informative biomarkers of aging in the field of human reproduction.

Acute myocardial infarction (AMI) remains a leading cause of morbidity and mortality worldwide. Ferroptosis, an iron-dependent form of regulated cell death, plays a crucial role in AMI progression. However, the molecular mechanisms regulating ferroptosis in AMI remain poorly understood. This study aims to investigate the role and potential regulatory mechanism of TAF15 in AMI. Bioinformatics analysis of gene expression datasets was conducted to identify differentially expressed genes in AMI samples. TAF15 expression was evaluated in clinical AMI patient blood samples, ischemia/reperfusion (I/R)-treated HL-1 cardiomyocytes, and myocardial tissues from the AMI mouse model using qRT-PCR and Western blot analyses. Gain- and loss-of-function experiments were performed to assess the effects of TAF15 and PRMT1 on myocardial injury, oxidative stress, and ferroptosis markers (Fe2⁺, MDA, GSH, GPX4, ROS) using electrocardiography, histopathology, CCK-8, EdU, TUNEL, ELISA, flow cytometry, qRT-PCR, and Western blot assays. Mechanistic studies, including luciferase reporter assays, chromatin immunoprecipitation (ChIP-qPCR), and bisulfite sequencing, were conducted to examine PRMT1-mediated TAF15 methylation and its regulatory effects. TAF15 was significantly downregulated in AMI, as observed in patient samples and experimental models. Functionally, TAF15 overexpression significantly improved myocardial function by inhibiting ferroptosis. Notably, TAF15 overexpression restored GPX4 and NRF2 expression, reduced Fe2⁺ accumulation and lipid peroxidation (MDA levels), and increased GSH levels in both HL-1 cardiomyocytes and AMI mouse model. Mechanistic investigations revealed that TAF15 interacted with NRF2, enhancing TAF15 transcription and subsequently activating the GPX4/NRF2 axis, which protects against ferroptosis-induced cardiomyocyte death. Additionally, PRMT1 negatively regulated TAF15 via hypermethylation. PRMT1 knockdown significantly upregulated TAF15 expression, leading to reduced ferroptosis and improved cardiac function. This study establishes TAF15 as a novel regulator of ferroptosis in AMI, activating the GPX4/NRF2 pathway to mitigate oxidative stress and myocardial injury. Furthermore, PRMT1-mediated TAF15 hypermethylation promotes ferroptosis, thereby exacerbating myocardial damage. These findings suggest that targeting the PRMT1/TAF15/GPX4-NRF2 axis represents a promising therapeutic strategy for AMI treatment by inhibiting ferroptotic cell death and improving cardiac function.

BackgroundCuproptosis, a form of cell death associated with copper ions, has been linked to the pathogenesis of various cancers, including gastric cancer. Investigating the role of cuproptosis-related genes through multi-omics analysis can enhance our understanding of disease mechanisms and improve prognosis prediction.ObjectiveThis study aims to elucidate the role of cuproptosis-related genes in gastric cancer from a multi-omics perspective.Materials and MethodsWe utilized multi-omics sequencing data from TCGA and GEO databases to explore the relationships between cuproptosis genes and gastric carcinogenesis, clinical phenotypes, and prognosis. This analysis encompassed mutation, copy number variation, methylation, mRNA expression, alternative splicing, and APA alterations. Additionally, we examined the regulatory roles of cuproptosis genes in gastric cancer through ceRNA interactions, gene mutations, and DNA methylation. A multi-omics prognostic model for gastric cancer was subsequently constructed.ResultsOur findings revealed that CDKN2A was the most frequently mutated gene in gastric cancer. Overall mutations in cuproptosis genes and copy number alterations of PDHB significantly impacted gastric cancer prognosis. Methylation, alternative splicing, and APA alterations of CDKN2A also influenced patient outcomes. Notably, MTF1, a key gene in cuproptosis, was found to affect apoptosis and invasion in gastric cancer cell lines.ConclusionWe successfully developed a multi-omics prognostic model for gastric cancer that offers significant predictive value for patient outcomes.

Acute lymphoblastic leukemia (ALL) is a prevalent malignant hematologic disease characterized by the abnormal proliferation and accumulation of immature lymphocytes in bone marrow and lymphoid tissues. In our study, Oxford Nanopore Technologies (ONT) sequencing was performed to investigate four types of methylation modifications—6 mA, CHG, CHH, and CpG—in a pair of monozygotic twins, where one twin has ALL and the other is healthy. The results showed the significant global hypomethylation of CpG sites and an increase in 6 mA, CHG, and CHH methylation in the twin diagnosed with ALL. Notably, the hypomethylation of CpG was particularly increased in the open sea, gene body, and 3'UTR regions, while 6 mA and CHG modifications exhibited high methylation levels in the gene body, TSS1500, TSS200, and 3'UTR regions. Additionally, CHH modifications showed high methylation across all genomic regions. Within the differential methylation loci (DML), we identified several genes related to tumorigenesis and progression (such as ZDHHC11, NBPF1, and TPTE). Furthermore, we systemically reviewed the literatures on leukemia and DNA methylation modifications, providing a comprehensive description of their correlation. In summary, these findings indicate that DNA methylation plays a crucial role in the onset and progression of ALL, offering valuable insights for future research into its impact on leukemia development.Graphic abstract

BackgroundImprinted genes are epigenetically regulated in normal tissues to follow monoallelic expression according to the parent of origin of each allele. Some of these patterns are dysregulated in cancer.ResultsWe developed a novel computational multi-omic pipeline to evaluate monoallelic and biallelic expression patterns based on matched RNA-seq expression data, whole-exome sequencing information, and copy number data. We analyzed allelic expression of the entire genes, individual isoforms, and each exon of 59,283 autosomal protein-coding and ncRNA genes, with a focus on 94 genes previously reported to be imprinted. We analyzed 108 cell lines from 9 different tumor histologies using molecular data from the DepMap Portal for the Cancer Cell Line Encyclopedia. Allelic expression patterns of imprinted genes and isoforms in tumor cells were variable. We also identified additional genes and isoforms with predominantly monoallelic expression due to a variety of potential mechanisms. We provide a novel public dataset of transcriptome-wide allelic expression patterns in cell lines from diverse tumor categories, which can serve as a resource for future cancer studies. We examined associations of in vitro cell line response to antitumor agents and repurposed drugs with allelic patterns and overall levels of isoform expression of imprinted genes and of additional genes with predominantly monoallelic expression. Drug response was associated with isoform expression patterns of multiple imprinted genes including CPA4, DGCR6, DNMT1, GNAS, GRB10, H19, NAA60, OSBPL5, PHACTR2, and ZFAT, predominantly monoallelically expressed MAP2K5 and BCLAF1, and additional predominantly monoallelically expressed genes. Multiple associations may be related to mechanisms of drug activity, including associations between the response to the DNA damaging agents and allelic expression of ZFAT, CDC27, and BCLAF1 isoforms, and the response to inhibitors of multiple signaling pathways with expression patterns of GNAS isoforms.ConclusionsTumor cells have a range of monoallelic and biallelic expression patterns in both imprinted and non-imprinted genes and are likely affected by the complex interplay among changes in allelic expression, sequence variants, copy number changes, and expression changes of biologically important genes. Multiple isoform-specific patterns of allelic expression were associated with drug response, indicating complex mechanisms of cancer chemoresistance.

BackgroundIn the therapeutic landscape of colorectal cancer (CRC), chemo-resistance poses a significant and prevalent obstacle that complicates treatment efficacy and patient outcomes. Over time, cancer cells can develop mechanisms to resist the toxic effects of chemo-therapy drugs, leading to reduced sensitivity or complete insensitivity to these agents. The enzyme Arylamine N-acetyltransferase 1 (NAT1) has emerged as a promising target in strategies aimed at overcoming this challenge. NAT1 is involved in the metabolism of various xenobiotics, including some chemotherapeutic agents. Understanding the complex interactions between NAT1 and chemotherapeutic agents, as well as the molecular mechanisms underlying chemo-resistance, is crucial for the development of novel therapeutic approaches. ObjectiveThis study aimed to assess the role of NAT1 in mediating chemo-resistance in CRC, with the goal of identifying novel strategies to overcome this clinical challenge.MethodsWe conducted a comprehensive analysis using various bioinformatics tools and in vitro experiments to evaluate the effect of NAT1 expression on chemo-resistance in CRC. Furthermore, we employed a multi-omics approach, including metabolomics and next-generation sequencing, to uncover the mechanisms by which NAT1 influences chemo-resistance. Additionally, we utilized single-cell RNA sequencing (scRNA-seq), the Cellchat assay, and western blot to explore the intercellular communication between tumor and endothelial cells in the context of anti-PD-1 therapy and NAT1’s impact.ResultsOur study reveals that decreased NAT1 expression in CRC tumor tissues, relative to adjacent normal tissues, is significantly associated with a poorer patient prognosis. Experimental data indicate that silencing NAT1 in CaCO2 and HCT116 cell lines results in heightened resistance to five chemotherapeutic agents: vinblastine, docetaxel, gemcitabine, vincristine, and daporinad. Additionally, NAT1 silencing increases the proportion of LGR5+ cells, which are known to be chemo-resistant. Our research further revealed that exposure to these five drugs induces a decrease in NAT1 expression within CRC cells. Mechanistic insights show that NAT1 knockdown triggers a metabolic reprogramming in CRC cells, shifting from oxidative phosphorylation and the tricarboxylic acid cycle to a preference for glycolysis. Furthermore, silencing of NAT1 in CRC cells leads to an up-regulation of VEGFA expression. Notably, the application of anti-PD-1 therapy was demonstrated to significantly disrupt the VEGFA-VEGFR axis signaling, an interaction critical between CRC cells and endothelial cells. This discovery underscores the potential of targeting the VEGFA pathway as a therapeutic approach to mitigate the adverse effects associated with NAT1 down-regulation in CRC.ConclusionOur study underscores the multifaceted role of NAT1 in modulating chemo-sensitivity, cellular metabolism, and angiogenesis in CRC. These findings position NAT1 as a compelling candidate for a biomarker and a potential therapeutic target, offering new avenues for CRC management.Graphical abstract

Abnormal DNA methylation is a hallmark of cancer and a nearly universal feature of melanoma. DNA methylation plays well-appreciated melanoma cell-intrinsic roles, including silencing tumor-suppressor genes, regulating genomic stability, deregulating expression of oncogenes to potentiate proliferative signaling and tumor migration. With the recent success of immunological therapies for melanoma, important roles for DNA methylation are also emerging at the interface between melanoma and immune cells with the potential to regulate the anti-tumor immune response. These newly recognized roles for DNA methylation in controlling melanoma cell immunogenicity, expression of MHC and immune checkpoint molecules as well as T cell phenotypes in the tumor microenvironment raise the possibility of using DNA methylation to develop improved therapies and methylation-based biomarkers. In addition to reviewing the “immune dimension” of DNA methylation, we summarize recent developments with potential clinical applications in melanoma, such as targeted DNA methylation editing, single-cell methylation approaches, and measurement of circulating methylated DNA. An improved understanding of the immune roles of DNA methylation presents an exciting opportunity for continued improvement of care and outcomes for patients with melanoma.

BackgroundAlthough DNA methylation age estimators (DNAmAges) are reliable tools for predicting aging, their effectiveness in predicting mortality risk has not been fully validated. This study compared the predictive utility of five different DNAmAges (HorvathAge, HannumAge, PhenoAgeAge, GrimAge and GrimAge2) for all-cause and cause-specific mortality among adults aged ≥ 50 years.MethodsWe screened 1966 participants adults aged ≥ 50 from the National Health and Nutrition Examination Survey (1999–2002) and linked them to the National Death Index to obtain cause and status of death. We used weighted Cox proportional hazards models to examine the associations between epigenetic age acceleration (EAA) measured by different DNAmAges and all-cause and cause-specific mortality in the general population, adjusting for various covariates including age, smoking status and chronic diseases. We used restricted cubic splines to explore nonlinear associations. Finally, stratified analyses were performed to assess the relationship between DNA age estimators and stratification variables.ResultsThe multivariable adjustment model showed that EAA measured by HorvathAge (AAHorvathAge), HannumAge (AAHannumAge), PhenoAge (AAPhenoAge), GrimAge (AAGrimAge) and GrimAge2 (AAGrimAge) were significantly associated with the risk of death, among which AAGrimAge and AAGrimAge2 had stronger statistical correlation and the correlation pattern was positively correlated. Specifically, each 5-year increase in AAGrimAge was associated with a 44% increased risk of all-cause death, a 33% increased risk of cardiovascular death and a 54% increased risk of non-cardiovascular death. And each 5-year increase in AAGrimAge2 was associated with a 40% increased risk of all-cause death, a 33% increased risk of cardiovascular death and a 47% increased risk of non-cardiovascular death. In contrast, AAHorvathAge, AAHannumAge and AAPhenoAge showed a J-shaped correlation with the risk of all-cause mortality and non-cardiovascular mortality, with the inflection points of all-cause mortality and non-cardiovascular mortality occurring at AAHorvathAge of 2.29 and 2.8, AAHannumAge of 3.07 and 2.97, and AAPhenoAge of − 7.65 and 7.04, respectively. No interaction was found between DNAmAges and stratification variables.ConclusionsAAGrimAge and AAGrimAge2 outperformed AAHorvathAge, AAHannumAge and AAPhenoAge in predicting mortality risk, and the association pattern was positive.

Immunotherapy, particularly immune checkpoint inhibitor therapy, has demonstrated clinical benefits in solid tumours. Despite its satisfactory clinical efficacy, it still faces several issues, such as limited eligibility, low response rates and cytotoxicity. Cancer epigenetics implies that tumour cells exhibit unique phenotypes because of their unique characteristics, thus reprogramming of the epigenome holds promise for cancer therapy. Epigenetic regulation plays an important role in regulating gene expression during tumour development and maintenance. Epigenetic regulators induce cancer cell cycle arrest, apoptosis and differentiation of cancer cells, thereby exerting anti-tumour effects. Recent studies have revealed a significant correlation between epigenetic regulatory factors and immune checkpoint therapy. Epigenetics can modulate various aspects of the tumour immune microenvironment and immune response to enhance the sensitivity of immunotherapy, such as lowering the concentration required and mitigating cytotoxicity. This review primarily discusses DNA methyltransferase inhibitors, histone deacetylase inhibitors, enhancer of zeste homolog 2 inhibitors and lysine-specific demethylase 1 inhibitors, which are associated with transcriptional repression. This repression alters the expression of genes involved in the immune checkpoint, thereby enhancing the effectiveness of immunotherapy. We also discuss the potential and challenges of tumour immunotherapy and highlight its advantages, application challenges and clinical research on integrating epigenetic regulatory factors with tumour immunotherapy.

Signal transduction plays a pivotal role in modulating a myriad of critical processes, including the tumour microenvironment (TME), cell cycle arrest, proliferation and apoptosis of tumour cells, as well as their migration, invasion, and the epithelial–mesenchymal transition (EMT). Epigenetic mechanisms are instrumental in the genesis and progression of tumours. The Chromobox (CBX) family proteins, which serve as significant epigenetic regulators, exhibit tumour-specific expression patterns and biological functionalities. These proteins are influenced by a multitude of factors and could modulate the activation of diverse signalling pathways within tumour cells through alterations in epigenetic modifications, thereby acting as either oncogenic agents or tumour suppressors. This review aims to succinctly delineate the composition, structure, function, and expression of CBXs within tumour cells, with an emphasis on synthesizing and deliberating the CBXs-mediated activation of intracellular signalling pathways and the intricate mechanisms governing tumourigenesis and progression. Moreover, a plethora of contemporary studies have substantiated that CBXs might represent a promising target for the diagnosis and therapeutic intervention of tumour patients. We have also compiled and scrutinized the current research landscape concerning inhibitors targeting CBXs, aspiring to aid researchers in gaining a deeper comprehension of the biological roles and mechanisms of CBXs in the malignant evolution of tumours, and to furnish novel perspectives for the innovation of targeted tumour therapeutics.