Accurate prognostic stratification remains a major challenge in colorectal cancer (CRC), as substantial heterogeneity in clinical outcomes persists even within the same pathological stage. While mutation-based circulating tumor DNA (ctDNA) analysis has transformed postoperative risk assessment by enabling detection of molecular residual disease (MRD), it primarily reflects the presence of tumor-derived genetic alterations and may not fully capture the biological processes underlying tumor progression. DNA methylation represents a complementary molecular layer that reflects coordinated regulatory states associated with tumor behavior, including transcriptional programs and cellular plasticity. Recent studies suggest that ctDNA methylation profiling may provide additional prognostic information beyond conventional clinicopathological factors and mutation-based assays, particularly in early-stage and postoperative settings. However, important challenges remain, including assay heterogeneity, lack of standardized metrics, and the need for robust external validation. In this Perspective, we examine the limitations of current prognostic frameworks and discuss the potential role of ctDNA methylation analysis as part of an integrated, multidimensional model for risk stratification in CRC. We propose that incorporating epigenetic information may refine prognostic assessment, while emphasizing the need for rigorous validation prior to clinical implementation.
The human genome contains hundreds of thousands of short open reading frames (sORFs), yet their translational products, hereafter referred to as sORF-encoded microproteins (also historically termed micropeptides), have long remained overlooked in conventional genome annotation. Increasing evidence demonstrates that these molecules play critical regulatory roles in human physiology and disease. This narrative review summarizes current knowledge regarding the classification, discovery, translational regulation, and biological significance of sORF-encoded microproteins. Their expression is tightly controlled by epigenetic mechanisms, including DNA methylation, Polycomb-mediated H3K27 trimethylation, and bivalent histone modifications, as well as epitranscriptomic regulation through N6-methyladenosine-mediated translation. Key microproteins such as Humanin, MOTS-c, Myoregulin, DWORF, HOXB-AS3-p, Mitoregulin, and CASIMO1 illustrate the diverse roles of sORF-derived peptides in cardiometabolic disease, neurodegeneration, and cancer. The review also highlights emerging therapeutic strategies, including epigenome editing, peptide replacement, and immunopeptidome-based neoantigen targeting. Collectively, the sORF-encoded microproteome represents an epigenetically integrated and functionally significant regulatory layer of the human proteome with major implications for fundamental biology and precision medicine.
BACKGROUND:Effective postoperative monitoring remains an important area of investigation for early-stage lung cancer patients after curative resection. This exploratory technical feasibility study evaluated a methylation-based fragmentomics approach by analyzing paired pre- and post-operative plasma cfDNA from 10 patients. RESEARCH DESIGN AND METHODS:Paired pre- and post-operative blood samples were collected from 10 patients with early-stage lung cancer who underwent curative-intent surgical resection. cfDNA was extracted, enriched for methylated fragments, and subjected to deep sequencing. Multidimensional cfDNA features including methylated cfDNA load, fragment length distribution, GC content, and copy number variations were analyzed. RESULTS:Postoperative samples showed decreased methylated cfDNA concentration and GC content. Fragment length analysis revealed a shift from shorter (mean 164 bp) to longer fragments (mean 200 bp) after surgery, along with the emergence of a ~ 336 bp sub-peak in postoperative samples. Methylation enrichment enabled detection of copy number variations that were attenuated post-operatively. CONCLUSIONS:Multi-dimensional cfDNA analysis can detect molecular changes after surgery in this small exploratory cohort. Further validation in larger prospective cohorts with longitudinal follow-up is warranted to assess potential clinical utility.
BACKGROUND:Associations between religiosity/spirituality (R/S) and health are well documented, but underlying mechanisms remain poorly understood. This review examined epigenetic and related molecular pathways that may underlie these associations. METHODS:EMBASE, PubMed, Web of Science, and Scopus were searched through 8 January 2025. Eligible studies assessed at least one R/S variable, construct, or intervention and gene-expression-related outcomes, including DNA methylation (DNAm), histone modifications, microRNAs, noncoding RNAs, or protein-level changes. Results were narratively synthesized. Risk of bias was assessed using Joanna Briggs Institute tools. RESULTS:Thirty-six studies were included, totaling 43,671 participants. Nineteen were cross-sectional, 22 were conducted in the United States, 23 involved community populations, and 10 included clinical samples. Overall, 39 instruments or measurement approaches assessed R/S. Outcomes included inflammatory, stress-related, lipid-related, and gene-regulatory markers, including C-reactive protein (CRP), interleukin-6, cortisol, lipid profile, DNAm, and messenger RNA. Findings were heterogeneous, with consistent inverse associations for CRP and a tendency toward lower cortisol with higher R/S, while other outcomes were mixed. DISCUSSION:The evidence suggests a potential beneficial epigenetics influence of R/S. However, methodological weaknesses, heterogeneity, limited longitudinal evidence, and small samples limit interpretation. Future studies require prospective designs, standardized measures, large samples, and confounding control. PROTOCOL REGISTRATION:www.crd.york.ac.uk/prospero identifier is CRD42022327728.
Diet is a key modifiable component of health, and a major risk factor for chronic disease in humans. At the molecular level diet can affect DNA methylation (DNAm), an epigenetic process that is involved in gene expression regulation. Multiple studies have linked DNAm profiles to changes in diet across different layers. Specifically, intake of nutrients such as folate and vitamin B12 has been associated with changes in human DNAm patterns genome-wide, linking dietary intakes to the potential modulation of gene activity. In this review we present a focused overview of recent findings from epigenome-wide association studies (EWAS) in human cohorts linking intake of specific vitamins to changes in the human methylome. We also discuss current gaps in knowledge and propose future directions to explore how exactly different components of diet influence the regulation of human gene function. One conclusion is the relative consistency of CpG-level DNAm signal replication in prenatal and early-life folate studies. In contrast, while biologically plausible, evidence from adult nutritional epigenome-wide association studies remains more heterogeneous. Ultimately, nutrition represents a powerful tool with the potential to support health and influence long-term biological processes through gene regulation, offering promising avenues for strategies aimed at disease prevention and healthy aging.
The output of an epigenetic aging clock can vary depending on the training method utilized, cell type composition, the nature of the training dataset, the technology used to generate the methylomic data, acute stressors, and other factors. On an individual level, epigenetic age can fluctuate across different clocks purely due to differences in model training. Among aging clock researchers, it is well-known that the epigenetic age of a single sample can vary across different models. Based on our observations and conversations with longevity scientists and stakeholders, however, this fact is often unappreciated among non-aging clock experts. To help bring more awareness to this important topic, we highlight key literature and, as an illustrative example, use eight blood-trained clocks to show that epigenetic age is frequently misaligned in a publicly available whole blood dataset. Our simple analysis revealed that the average sample difference between the youngest and oldest predicted ages across these clocks was 17 years. The smallest and largest individual-level differences observed were 4 and 45 years, respectively. Clock misalignment has implications for choosing which clock to utilize, interpreting the impact of an intervention on epigenetic age, personalized tracking, and relating epigenetic age to the abstract concept of biological age.
Chronic pain represents a major public health challenge, imposing a substantial burden on both patients and healthcare systems. Beyond genetic predisposition, accumulating evidence indicates that epigenetic mechanisms contribute to the development and persistence of chronic pain disorders. Among these, DNA methylation and long non-coding RNAs (lncRNAs) have emerged as important regulators of gene expression involved in pain-related biological processes. This review integrates recent findings on epigenetic alterations in chronic pain disorders, including chronic primary pain conditions such as chronic low back pain, fibromyalgia, myalgic encephalomyelitis/chronic fatigue syndrome and migraine, and chronic secondary pain conditions, including rheumatoid arthritis, osteoarthritis and neuropathic pain. We highlight how disease-associated changes in DNA methylation and lncRNA expression influence pathways related to inflammation, nociceptive signaling and central sensitization, thereby contributing to pain susceptibility and maintenance. In addition, we discuss the emerging use of DNA methylation-based epigenetic clocks to estimate biological age in chronic pain disorders, with potential applications as biomarkers for disease risk, prognosis and patient stratification. Furthermore, we address histone modifications as an underexplored epigenetic layer in human chronic pain. Finally, we consider how lifestyle and environmental factors shape epigenetic regulation and discuss how targeting them may optimize personalized strategies for managing chronic pain.
DNA methylation at CpG dinucleotides represents a key epigenetic mechanism linking genetic variation to gene regulation in complex human diseases. Single-nucleotide polymorphisms (SNPs) that create or disrupt CpG sites can alter local DNA methylation and transcriptional activity, thereby influencing disease susceptibility. These CpG-modifying variants provide a functional interface between inherited genetic variation and epigenetic regulation in complex metabolic disorders. This review summarizes current evidence on SNP-derived CpG variation and its role in allele-specific DNA methylation and gene regulation in metabolically relevant tissues. By integrating findings from genome-wide association studies, epigenome-wide association studies, and multi-omics research, this review provides a mechanistic framework explaining how CpG-modifying polymorphisms influence adipogenesis, pancreatic β-cell function, inflammation, and glucose metabolism. Special emphasis is placed on South Asian populations, who exhibit early β-cell dysfunction and increased visceral adiposity. Many CpG-modifying variants act as methylation quantitative trait loci (meQTLs), influencing allele-specific methylation and gene expression. Understanding SNP-CpG-methylation interactions may improve functional interpretation of disease-associated genetic variants, enhance biomarker discovery, and support precision medicine strategies for metabolic disease.
BACKGROUND:Measures of biological aging based on DNA methylation (epigenetic clocks) are commonly used in research across the biological, health, and social sciences. Many decisions are made during the quality control (QC) of the data on which such clocks are based, generating removed beta values that must be accommodated in construction of the clocks. METHODS:We apply a range of detection p-value and bead count thresholds during QC of a DNA methylation dataset and characterize the removed beta values. We then test different methods of imputing removed beta values and their impact on epigenetic clocks. RESULTS:We find that both detection p-value and bead count thresholds remove beta values that differ significantly in their distribution from the values retained post-QC. Epigenetic clocks calculated from datasets using various imputation methods (mean, median, KNN, and methyLImp) do not appear to have consistent patterns of bias. The only exception is imputation of 0 for removed beta values (akin to leaving out those CpGs on a per-sample basis when calculating clocks), which shows stronger proportional bias of clock values for all clocks. CONCLUSION:We recommend imputing removed beta values rather than leaving those CpGs out of clock calculations on a per-sample basis.
BACKGROUND:Preeclampsia (PE) is a serious pregnancy complication with elusive pathogenesis. Although epigenetic dysregulation is implicated, its layer-specific placental roles are poorly defined. This study aimed to identify shared and layer-specific epigenetic alterations in PE by profiling DNA methylation and gene expression in placental villi (PV) and chorioamniotic membranes (CAM). RESEARCH DESIGN AND METHODS:PV and CAM samples were collected from 7 normal and 8 PE pregnancies, and three public DNA methylation datasets (GSE98224, GSE44667, GSE75196) were integrated. Differentially methylated genes (DMGs) and differentially expressed genes (DEGs) were identified based on whole-genome methylation and transcriptome sequencing. Layer-specific and shared gene sets were identified by cross-analysis, with functional annotation using Gene Ontology (GO). RESULTS:EM-seq revealed a hypermethylation-dominant, tissue-specific methylation landscape in PE placentas. Cross-tissue comparison identified shared DMGs between the two layers, including nine key genes consistently altered in public datasets. Integrated analysis in PV further identified 22 co-dysregulated genes, enriched in thermoregulation, maternal-fetal immunity, signal transduction, and cell differentiation. CONCLUSIONS:This study elucidates the shared and layer-specific dysregulation of gene networks at methylomic and transcriptomic levels in PE placenta. Comparing PV and CAM highlights placental epigenetic heterogeneity and dysfunction, offering novel clues for mechanistic research and layer-targeted therapies.
Background Epithelial-mesenchymal transition (EMT) and glycolysis contribute to breast cancer (BC). However, the molecular mechanisms underlying these processes require further investigation.Methods Gene abundance was determined using RT-qPCR, Western blotting, and IHC. Cell viability and migration were evaluated using CCK-8 and scratch tests. Co-IP was performed to confirm the RNF125-HDAC1 interaction. Glycolysis-related indicators were detected using commercial kits, the Seahorse XF assay, and Western blotting. The enrichment of H3K27ac in the PGM5 promoter was determined using ChIP.Results In BC samples, RNF125 and PGM5 levels were downregulated, whereas HDAC1 expression was upregulated. Upregulation of RNF125 inhibited EMT and glycolysis in BC cells, suppressed tumor growth in subcutaneous tumor-bearing mouse models, and reduced lung metastasis in mice; these effects were counteracted by HDAC1 overexpression. Similarly, PGM5 overexpression suppressed EMT and glycolysis in BC cells; however, this suppression was blocked by HDAC1 overexpression or RNF125 knockdown. Mechanistically, RNF125 promoted HDAC1 ubiquitination, leading to its proteasomal degradation. Moreover, HDAC1 reduced PGM5 expression by inhibiting H3K27ac enrichment at the PGM5 promoter.Conclusion RNF125 suppressed EMT and glycolysis in BC cells and delayed tumor growth in subcutaneous tumor-bearing mouse models, as well as lung metastasis in mice through modulation of the HDAC1/PGM5 axis.
The Mendelian disorders of the Epigenetic Machinery (MDEMs), or Chromatinopathies, are now understood to be a collectively common cause of childhood neurodevelopmental delays and intellectual disability. In the past decade, the chromatin and gene expression consequences of heterozygous chromatin regulator disruption have been investigated in various disease models, yielding insights into the molecular pathogenesis of MDEMs. In this review, we highlight some of these results - drawing upon studies of representative MDEMs - together with potential unifying concepts. We propose that MDEMs are characterized by distributed, often subtle chromatin and gene expression perturbations, which impact diverse cellular pathways and processes and are frequently shared between distinct disorders. In this sense, they occupy an intermediate space between classical monogenic disorders and complex traits. We propose potential explanations for the variable expressivity in MDEMs and conclude by considering how technological advances can now enable a deeper and more precise mechanistic characterization of this important Mendelian disease group.
Cancer cells reprogram their metabolic networks to sustain continuous proliferation, resist stress, and support invasive behavior. This metabolic rewiring includes enhanced aerobic glycolysis, increased glutaminolysis to fuel biosynthetic reactions, activation of the pentose phosphate pathway (PPP) for nucleotide synthesis and redox balance, and reorganization of lipid metabolism to integrate membrane biogenesis and energy adaptation. While several oncogenes are well established as metabolic regulators, it is increasingly recognized that non-coding RNAs also contribute to the control of tumor metabolic phenotypes. Among them, the long non-coding RNA (lncRNA) HOX transcript antisense intergenic RNA (HOTAIR) has emerged as one of the most consistently upregulated and functionally relevant lncRNAs in human cancers. Accumulating evidence links HOTAIR to metabolic reprogramming in diverse tumor types. HOTAIR controls the expression and activity of key glycolytic enzymes and regulates lipogenesis, lipid accumulation, and metastatic lipid remodeling. However, findings remain dispersed across individual studies, and a consolidated framework integrating HOTAIR regulation with major metabolic pathways is currently lacking. This review synthesizes current knowledge on how HOTAIR drives metabolic rewiring in cancer, with a focus on carbohydrate and lipid metabolism, and discusses the underlying molecular mechanisms and therapeutic implications.
Background Early life adversity is associated with increased cardiometabolic risk across the life course, potentially via epigenetic mechanisms. However, few studies have prospectively examined how distinct domains of early life adversity influence molecular profiles and cardiometabolic health.Research design and methods In the CHAMACOS cohort, a longitudinal study of rural Latino youth, we measured adversity prospectively from pregnancy through age 7 across six domains: Learning Environment, Parent-Child Interaction, Maternal Adversity, Family Dysfunction, Economic Adversity, and Stressful Life Events. Leukocyte DNA methylation (DNAm) was measured at four timepoints between ages 7 and 18, gene expression (RNA transcripts) at age 14, and body mass index (BMI) and insulin resistance (HOMA-IR) at age 18.Results Early life adversity was associated with differential DNAm at ages 7, 14, and 18, with 14 Bonferroni- and 101 FDR-significant differentially methylated probes (DMPs) across all timepoints. Economic adversity was the domain most strongly associated with DMPs (4 Bonferroni- and 38 FDR-significant). Methylation changes at several DMPs were significantly associated with BMI and HOMA-IR at age 18.Conclusions These findings provide longitudinal evidence that early life adversity, particularly economic adversity, becomes biologically embedded via DNAm, with functional and cardiometabolic consequences, highlighting potential targets for early interventions to reduce lifelong disease risk.
Genome-wide approaches have unveiled multiple aspects of primary brain and spinal cord cancers regarding oncogenic processes, the tumor microenvironment, and mechanisms of resistance and sensitivity to therapy (among many others). In this review, we provide a brief overview of the possibilities that the current and highly diverse omics techniques offer for genomic landscape characterization, and how they can enhance our understanding of gliomas and glioneuronal tumors. More specifically, we discuss available methodologies for transcriptomics profiling (gene expression, alternative splicing, RNA modifications) and epitranscriptomics profiling (DNA methylation and hydroxymethylation, histone covalent modifications, chromatin accessible regions) at the level of bulk tissue, sorted and single cells, and biofluids. Multiomics integration of cancer-associated molecular alterations, including mapping of long-distant DNA interactions, enables a better understanding of tumor biology, providing clues concerning patient stratification, biomarker discovery, identification of key oncologic players with clinical utility, and potential novel therapeutic interventions. Furthermore, these multiomics have generated diverse and extensive databases that are available to the scientific community. Finally, we discuss that widespread implementation of omics into the clinic is still challenging but holds good prospects for effectiveness in the near future.
BACKGROUND:Early and accurate detection of bladder cancer (BCa), particularly low-grade and early-stage disease, remains challenging because current diagnostic methods are either invasive or insufficiently sensitive. We aimed to develop a noninvasive urine DNA methylation assay for BCa detection and postoperative monitoring. RESEARCH DESIGN AND METHODS:Integrative methylation profiling across institutional and public cohorts identified PENK and NKPD1 as urothelial carcinoma-associated hypermethylation markers. A bisulfite-free methylation-sensitive restriction enzyme quantitative polymerase chain reaction (MSRE-qPCR) assay was developed using urine sediment DNA. Diagnostic performance was evaluated in a case-control cohort of 606 urine samples, including 340 pathologically confirmed BCa cases. RESULTS:The dual-marker assay achieved areas under the curve (AUCs) of 92.52% and 93.00% in the training and validation cohorts, respectively. Sensitivity reached 87.74%, with specificity of 92.31% against benign urological diseases and 83.05% against non-urothelial malignancies. The assay outperformed urine cytology in low-grade tumors and provided complementary diagnostic value when combined with cytology. Postoperative methylation signals significantly decreased after tumor resection (p < 0.001). CONCLUSIONS:This bisulfite-free urine MSRE-qPCR assay provides a simple and scalable approach for noninvasive BCa detection and surveillance, with strong performance in early-stage and low-grade disease. Further prospective multicenter validation is warranted.
Tumor suppressor genes and DNA repair genes can be inactivated not only by genetic lesions, like mutations or deletions, but also by aberrant DNA methylation of promoter regions. These DNA methylation alterations may serve as biomarkers for early detection, refinement of diagnosis, prognosis, or prediction of therapy response. Despite a long history of DNA methylation research in the field of oncology so far only very few aberrant DNA methylation events are of proven and generally accepted clinical value and are part of the routine diagnostic work‑up of cancer patient samples. Hypermethylation of the MGMT gene promoter in glioblastoma is one of the very few DNA methylation biomarkers that has entered routine clinical diagnostics. In this very aggressive primary brain tumor it is associated with an overall better prognosis and a better response to alkylating therapy. This narrative review provides an overview about the underlying biology, the methodological challenges, and the clinical utility of MGMT promoter methylation, primarily in the context of glioblastoma. Emerging applications in other cancer types are also summarized and discussed. Throughout the review the focus is more on a critical discussion of concepts and relevant publications and their merits and shortcomings than trying to achieve complete coverage of the voluminous literature.
Isocitrate dehydrogenase (IDH)-wildtype glioblastoma is an aggressive brain tumor characterized by limited therapeutic options and poor survival outcomes. Beyond well-established genomic alterations, epigenetic mechanisms such as DNA methylation have gained attention for their roles in glioblastoma pathogenesis. Tumor suppressor genes are frequently silenced through promoter hypermethylation, whereas global hypomethylation of repetitive elements contributes to genomic instability and oncogenic progression. Clinically, O6-methylguanine-DNA methyltransferase (MGMT) promoter methylation remains an important biomarker for predicting patient response to alkylating chemotherapies. Advances in single-cell epigenomic sequencing have characterized the remarkable heterogeneity of DNA methylation within glioblastoma. Techniques including single-cell bisulfite sequencing (scBS-seq) and single-cell reduced representation bisulfite sequencing (scRRBS) provide high-resolution insights into the methylation landscapes of individual tumor cells. These analyses reveal that epigenetic diversity underlies subclonal expansion, therapy resistance, and tumor recurrence. Moreover, integrating single-cell methylation data with other modalities such as transcriptomics and proteomics offers a multidimensional view of tumor evolution and microenvironmental dynamics. Despite ongoing challenges in cost, data interpretation, and large-scale integration, single-cell epigenomics has potential applications in refining glioblastoma classification and guiding personalized therapeutic strategies in the future. This review explores emerging roles of DNA methylation in glioblastoma alongside cutting-edge single-cell techniques and translational prospects.
