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}NCBI GEO2026 · Methylation profiling by genome tiling array · 40 samples
DNA Copy Number Analysis of Germ Cell Tumors in the Thai PopulationThis project aims to identify CNVs of intracranial and extracranial germ cell tumors in the Thai population. Formalin-fixed paraffin-embedded tissues (FFPET) from intracranial (IGCTs) and extracranial germ cell tumors (EGCTs) were extracted and analyzed using SNP microarray, and somatic CNVs were also investigated. Pathway enrichment analysis and associations between significant CNVs, clinical par
NCBI GEO2026 · Methylation profiling by genome tiling array · 8 samples
Functional Merlin Depletion Defines a TEAD1-Dependent Tumor Cell State that Promotes Schwannoma Progression: bulk methylationBiallelic loss of the tumor suppressor NF2/merlin drives vestibular schwannomas (VS). Intratumoral heterogeneity has been observed in VS at the transcriptional, protein expression, and cellular proliferative potential levels, highlighting the need to elucidate the mechanisms underlying heterogeneity in tumor Schwann cell merlin inactivation and therapeutic resistance. Using integrated single-cell
NCBI GEO2026 · Methylation profiling by genome tiling array · 32 samples
Methylation profiling in colorectal cancer: colorectal cancers vs. adjacent normal colon tissuesDysregulation of cellular metabolism is one of the hallmarks of cancer. Tumor cells would enhance glycolysis to fuel the phenotypes of rapid proliferation and invasion. This study aims to explore epigenetic reprogramming of glycolysis pathway in colorectal cancer (CRC). CRCs and the adjacent normal colon tissues were profiled by using a comprehensive methylation array (Illumina Methylation EPIC Be
NCBI GEO2026 · Methylation profiling by genome tiling array · 82 samples
Genome-wide DNA Methylation Profiling in Postpartum Depression: A Longitudinal Whole-Blood StudyThis dataset contains genome-wide DNA methylation data derived from whole human blood samples collected from postpartum women enrolled in a longitudinal cohort study (2018–2023, N = 827). Blood samples were drawn within 6 days of delivery (t0) and at 12 weeks postpartum (t4). Participants were assessed longitudinally for postnatal depression (EPDS), perceived stress (PSS-10), and mother-infant att
NCBI GEO2026 · Methylation profiling by genome tiling array · 75 samples
Epigenetic Age Acceleration Enhances Prediction of Overall Survival in Early-Stage Non-Small Cell Lung CancerEpigenetic age, influenced by environmental factors like smoking, predicts mortality in general populations but remains under-explored in early-stage lung cancer. We analyzed blood DNA methylation from 75 Boston Lung Cancer Study participants with early-stage non-small cell lung cancer (NSCLC), of whom 63 died during follow-up. Epigenetic age acceleration (EAA) was estimated using Horvath, Hannum,
NCBI GEO2026 · Methylation profiling by genome tiling array · 30 samples
Epigenetic and Immunological Alterations in Umbilical Cord Blood of Overweight/Obese Women with Gestational Diabetes Mellitus: Insights into DNA Methylation Signatures and Immune Cell DysregulationGestational diabetes mellitus (GDM) is a prevalent pregnancy complication with significant maternal and fetal health implications. This study examines the impact of overweight/obesity-related GDM on DNA methylation and immune function in umbilical cord blood. Using an 850K methylation array, we identified 23,331 hypermethylated and 29,501 hypomethylated differentially methylated positions (DMPs),
NCBI GEO2026 · Methylation profiling by genome tiling array · 19 samples
Decitabine-induced CD38 upregulation augments daratumumab activity in xenograft T-ALLThis study investigates epigenetic regulation of CD38 in T-cell acute lymphoblastic leukemia (T-ALL) and the effect of decitabine (DEC) on CD38 promoter methylation and CD38 expression. Genome-wide DNA methylation profiling was performed in T-ALL cell lines treated with DEC or DMSO and in baseline T-ALL patient-derived xenograft (PDX) samples using the Illumina Infinium MethylationEPIC BeadChip v2
NCBI GEO2026 · Methylation profiling by genome tiling array · 8 samples
A MAGIBU-BASED MODEL FOR PEDIATRIC AND JUVENILE CNS TUMORS: AN IN-HOUSE EPIGENETIC DECISION-SUPPORT FRAMEWORK COMPARED WITH ONLINE DNA METHYLATION CLASSIFIERSDNA methylation profiling is widely used for CNS tumor classification. We developed MAGIBU, an in-house framework that integrates DNA methylation data via UMAP projection onto a reference CNS tumor landscape and ranks tumor classes based on epigenetic proximity. Rather than providing pre-defined diagnoses, MAGIBU offers quantitative information to support integrative assessment. We evaluated MAGIB
NCBI GEO2026 · Methylation profiling by genome tiling array · 205 samples
Clinical Evaluation of the CrossNN DNA Methylation Classifier for Central Nervous System TumorsBackground: DNA methylation profiling has become an integral diagnostic tool in the classification of central nervous system (CNS) tumors. While the Heidelberg CNS Tumor Methylation Classifier is widely adopted in clinical practice, new classifiers such as CrossNN are emerging. However, the clinical interpretation and added value of these tools within current practices are insufficiently explored.
NCBI GEO2026 · Methylation profiling by genome tiling array · 9 samples
Locus-selective targeting of the oncogenic fusion EWSR1-FLI1 in Ewing Sarcoma by CRISPR/dCas9 silencers [DNA methylation]Despite the revolutionary impact of genome engineering tools in medicine, the safe and effective intracellular delivery of CRISPR remains a major obstacle for clinical applications. Here, we utilize precision molecular targeting and delivery strategies based on CRISPR/dCas9 systems adapted for epigenetic repression (dCas9-KRAB) to silence oncogenic drivers with high selectivity. As proof-of-princi
NCBI GEO2026 · Methylation profiling by genome tiling array · 47 samples
Epigenetic markers of tumor progression in breast cancer patients with high nodal involvementBackground: Management of axillary lymph node (LN) disease in breast cancer (BC) is evolving, with declining use of axillary lymph node dissection (ALND). Consequently, prognostic information from nodal assessment is becoming limited. Molecular determinants of primary tumors associated with greater nodal burden could provide complementary prognostic value and mechanistic insights into progression.
NCBI GEO2026 · Methylation profiling by genome tiling array · 1 samples
Nanopore and EPIC Array Profiling Unmask an Atypical Non-Midline H3 K27-Altered Glioma: a case reportWe report a rare adult case of H3K27-altered diffuse glioma arising in an atypical non-midline location, highlighting the diagnostic challenges posed by its radiological and histopathological resemblance to glioblastoma. The study demonstrates the clinical utility of integrated histopathological, methylation-based, and genomic analyses, including rapid Nanopore methylation profiling, for accurate
NCBI GEO2026 · Methylation profiling by genome tiling array · 723 samples
Association of Epigenetic Trajectory With Development of Clinical Rheumatoid Arthritis in Individuals With Anti–Citrullinated Protein Antibody Positivity: Targeting Immune Responses for Prevention of Rheumatoid Arthritis (TIP-RA)The presence of autoantibodies to citrullinated protein antigens (ACPAs) in the absence of clinically-apparent inflammatory arthritis (IA) identifies individuals “at-risk” for developing future clinical rheumatoid arthritis (RA). However, it is unclear why some ACPA+ individuals convert to clinical RA while others do not. We explored the possibility in the Targeting Immune Responses for Prevention
NCBI GEO2026 · Methylation profiling by genome tiling array · 28 samples
Intratumoral DNA Methylation Heterogeneity as a Determinant of Metastatic dissemination in Endometrial CancerIntratumoral heterogeneity is a central determinant of tumor progression and metastasis across multiple cancers, however, its epigenetic architecture remains insufficiently defined. DNA methylation heterogeneity represents a critical but largely underexplored layer of regulatory complexity in endometrial cancer (EC), with potential implications for tumor behavior and clinical outcome. Most studies
NCBI GEO2026 · Methylation profiling by genome tiling array · 220 samples
Next-GenerationPediatric Cancer Models: Patient-Matched Orthotopic Xenografts, 3D Organoids, 2D Cultures, and Cell Lines for Identification of Therapeutic Vulnerabilities in Pediatric Solid TumorsMost pediatric solid tumor cell lines were established decades ago, so patient-matched organoids and xenografts are not available, limiting their translational utility. Here, we present a new approach to generate triads of patient-matched xenografts, 3-dimensional (3D) organoids, and 2D cultures. We have generated 3D organoids from 135 pediatric tumors, including rhabdomyosarcoma, osteosarcoma, ne
NCBI GEO2026 · Methylation profiling by genome tiling array · 8 samples
Comparative DNA methylation profiling of highly invasive and parental patient-derived glioblastoma stem-like cells using the Illumina Infinium MethylationEPIC arrayThis dataset contains genome-wide DNA methylation profiles of patient-derived glioblastoma stem-like cells (GSCs) generated using the Illumina Infinium MethylationEPIC BeadChip array. A highly invasive subpopulation was established by serial transwell invasion selection and compared with the parental, non-selected population. The dataset was generated to identify DNA methylation changes associated
NCBI GEO2026 · Methylation profiling by genome tiling array · 118 samples
Distinct DNA Methylation Changes Following A Superset And Repeated Sprint Training Intervention In Youth Male Basketball Players: A Genome-Wide DNA Methylation StudyUnderstanding the process of adaptation remains a key challenge for strength coaches to enhance athletic performance in basketball players. While physical improvements are commonly used to track progress, these adaptations are underpinned by tightly regulated molecular changes within skeletal muscle. Among these, DNA methylation is an epigenetic mechanism that modulates gene expression in response
NCBI GEO2026 · Methylation profiling by genome tiling array · 3 samples
Spinal low-grade ependymal tumors harboring telomerase reverse transcriptase promoter mutation and chromosome 7 gain with methylation profile of spinal subependymomaSpinal intramedullary tumors comprise a heterogeneous group of entities with diverse histopathological features, making their diagnosis particularly challenging. In this study, we identified three cases of spinal ependymal tumors exhibiting a methylation profile of spinal (SP-) subependymoma (SEPN). One case exhibited histopathological features and a methylation profile typical of SP-SEPN, whereas
NCBI GEO2026 · RNA sequencing · 89 samples
IL-15 Signaling During a Critical NK Cell Developmental Window Subverts Maturation and KIR AcquisitionThis SuperSeries is composed of the SubSeries listed below.
NCBI GEO2026 · Methylation profiling by genome tiling array · 66 samples
IL-15 Signaling During a Critical NK Cell Developmental Window Subverts Maturation and KIR Acquisition [Methylation array]Natural killer (NK) cells are key mediators of immune surveillance following hematopoietic stem cell transplantation (HSCT). However, despite the known post-conditioning spike in interleukin-15 (IL-15), NK cell maturation is frequently delayed following HSCT. We found that during in vitro NK cell development from CD34+ hematopoietic progenitor cells (HPCs), early exposure to IL-15 drove aberrant m
NCBI GEO2026 · Methylation profiling by genome tiling array · 35 samples
Human Tumor Atlas Pilot Project (HTAPP) neuroblastoma methylation array datasetsGenome-wide methylation profiling of 35 neuroblastomas that are part of the HTAPP neuroblastoma cohort. Data was generated using the Illumina MethylationEPIC 850k bead array.
NCBI GEO2026 · Methylation profiling by genome tiling array · 8 samples
Engineering epicardium-integrated human iPSC-derived heart tissue for modelling Hutchinson-Gilford Progeria Syndrome [Infinium Methylation EPIC]Engineered heart tissues (EHT) have been utilized in research for almost three decades and have become an important tool in cardiovascular research to address the shortcomings of the interspecies issues of animal models and oversimplicity of single cell type two-dimensional cell models to recapitulate cardiac (patho)physiology. Recently, epicardium-integrated EHT models have emerged in research as
NCBI GEO2026 · Methylation profiling by genome tiling array · 30 samples
Transcriptomic reprogramming screen identifies SRSF1 as a regulator of aging - EPICAging is characterized by progressive functional decline accompanied by distinct transcriptomic and epigenetic alterations. Although partial reprogramming via Yamanaka factors can reverse these signatures and improve cell function, toxicity and efficacy concerns limit their in vivo application, necessitating alternative geroprotective interventions. Here, we develop an interpretable transcriptomic
NCBI GEO2026 · Methylation profiling by genome tiling array · 169 samples
Methylome profiling of cartilage tumors: a promising new diagnostic tool?DNA methylation and copy number variation (CNV) profiling has emerged as a promising tool for the classification of bone and soft tissue tumors. We evaluated its utility in cartilage tumors, where distinguishing low-grade from high-grade conventional central chondrosarcoma (CS) as well as atypical cartilaginous tumors (ACT) from enchondromas are frequent diagnostic challenges, particularly on biop
NCBI GEO2026 · Methylation profiling by genome tiling array · 42 samples
Distinct epigenetic alterations and accelerated mitotic aging define second primary breast cancersSecond primary breast cancers (SPBCs) are becoming increasingly common among cancer survivors and are linked to poorer clinical outcomes compared to first primary breast cancers (FPBCs). While the molecular features of FPBCs are well characterized, the biological underpinnings of SPBCs remain largely unexplored. SPBC tumors exhibited 11,321 differentially methylated CpG sites compared to FPBCs, wi