Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

REMODEL: A modular framework for longitudinal ctDNA methylation profiling reveals treatment response and relapse-associated epigenetic remodeling

ABSTRACT: Circulating tumour DNA (ctDNA) methylation profiling is a promising non-invasive tool for disease monitoring, but longitudinal interpretation is limited by variable sequencing coverage and the loss of clinically relevant signals. We developed REMODEL (Recovery-based Epigenetic Monitoring of Dynamic methylation for Longitudinal analysis), an integrated framework combining coverage-aware binning, count-based longitudinal statistics, and a novel Epigenetic Recovery Score (ERS) to quantify post-treatment methylation recovery. Applied to 17 serial plasma samples from two T-cell lymphoma patients (2,025 genomic bins), REMODEL distinguished durable remission, characterized by coordinated demethylation (86.4% of bins) and sustained positive ERS, from relapse, marked by widespread hypermethylation (64.9% of bins) and persistently negative ERS despite clinical remission. By integrating dynamic methylation detection with recovery modelling, REMODEL provides an interpretable framework for longitudinal ctDNA methylation analysis and minimal residual disease monitoring.

ORGANISM(S): Homo sapiens

PROVIDER: GSE342177 | GEO | 2026/08/06

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other
	GSE342177_RAW.tar	Raw
	GSE342177_processed_data.tar.gz	Other
	filelist.txt	Txt

Items per page:

1 - 4 of 4

Similar Datasets

Dynamic Monitoring of ctDNA Methylation to Predict Relapse in Colorectal Cancer After Radical Resection (POSTCA)

Project description:This is a prospective, multicenter, observational, single-blinded controlled study. Dynamic monitoring of patients with resectable colorectal cancer was performed using the previously established colorectal tumor-specific plasma ctDNA methylation markers (Multigene methylation detection). Dynamic monitoring of plasma ctDNA methylation before and after treatment and at regular follow-up in patients with colorectal cancer after radical resection of tumor, to explore the predictive effect of postoperative plasma ctDNA methylation on postoperative recurrence and whether dynamic monitoring of postoperative ctDNA methylation could be earlier than imaging examination to indicate tumor recurrence.

| 2289240 | ecrin-mdr-crc

Long-term longitudinal analysis of peripheral blood transcriptome in COVID-19 patients

Project description:We performed the longitudinal peripheral blood transcriptome profiling after diagnosis in five patients, and found that patients' blood transcriptomes undergo dramatic and consistent changes in early recovery stage (ERS). Meanwhile, the blood transcriptome did not fully return to the healthy state even after more than one month of recovery. We also realized that differential expressed genes (DEGs) are enriched in biological processes of antigen processing and related processes, and promoter regions of these genes enrich key transcription factors (TFs) involved in T cell differentiation and activation. We further provided potential mechanisms underlying these orchestrated processes, by revealing these specific TFs mediated gene co-expression network.

2022-04-12 | GSE154272 | GEO

Evolutionary pressures shape undifferentiated pleomorphic sarcoma development and radiotherapy response.

Project description:Although radiotherapy plays a crucial role in treating many cancers, the effect of radiation on tumor evolution remains unclear. We integrated temporal genomic profiling of 120 spatially distinct tumor regions from 20 patients with undifferentiated pleomorphic sarcomas (UPS), longitudinal circulating tumor DNA (ctDNA) analysis, and evolutionary biology computational pipelines to study UPS evolution during tumorigenesis and in response to radiotherapy. Most unirradiated UPS displayed initial linear evolution followed by subsequent branching evolution with distinct mutational processes during early and late development. Using metrics of genetic divergence between regions, we demonstrated evidence of strong selection pressures during UPS development that further increased during radiotherapy. We observed changes in subclone abundance following radiotherapy with subclone contraction tied to alterations in calcium signaling and demonstrated that inhibiting calcium transporters can radiosensitize sarcoma cells. Finally, ctDNA analysis accurately measured subclone abundance and enabled non-invasive monitoring of subclonal changes. These results demonstrate that radiation exerts selective pressures on UPS and suggest that targeting radioresistant subclonal populations could improve outcomes after radiotherapy.

2024-12-13 | GSE279683 | GEO

Predictive Value of ctDNA for NED Status in mCRC and Its Utility in Guiding Therapeutic Intervention

Project description:The goal of this clinical trial is to detect the prognostic value of longitudinal monitoring circulating tumor DNA (ctDNA) for no evidence of disease (NED) status in metastatic colorectal cancer (mCRC) patients and its utility in guiding therapeutic intervention. The main questions it aims to answer are: 1. Whether ctDNA monitoring could evaluate NED status ahead of normal radiologic monitoring. What about the concordance of evaluating NED status by ctDNA monitoring compared with normal radiologic monitoring? 2. Whether the patients with ctDNA positive status could benefit from early therapeutic intervention. Patients who receive any kinds of therapies with the aim of NED and are confirmed by clinical and radiologic examination will go through longitudinal ctDNA monitoring. According to the results of ctDNA monitoring, the patients will be divided into ctDNA positive group and ctDNA negative group. Patients in ctDNA positive group will receive individual therapeutic plan decided by the investigator. Patients in ctDNA negative group will receive regular examinations. When radiologic recurrences are confirmed, the patients will be re-evaluated for a second opportunity of radical resection.

| 1231 | ecrin-mdr-crc

Circulating tumor DNA for monitoring classic Hodgkin lymphoma patients: correlation with FDG-PET/CT

Project description:Circulating tumor DNA (ctDNA) as a biomarker of disease activity in classic Hodgkin lymphoma (cHL) patients are still not well-defined. By profiling primary tumors and ctDNA, we identified common variants between primary tumors and longitudinal plasma samples in most of the cases, confirming high PBatial and temporal heterogeneity. Though ctDNA analyses mirrored HRS cell genetics overall, the prevalence of variants shows that none of them can be used as a single biomarker. Conversely, the estimation of hGE/mL, based in total ctDNA quantification, reflects disease activity and is almost perfectly correlated with standard parameters such as PET/CT that are associated with refractoriness.

2023-12-18 | GSE244989 | GEO

Analysis of ctDNA methylation induced by ionizing to different ograns

Project description:This study aims to compared ctDNA methylation status induced by ionizing to different ograns. SD rats were irradiated with local radaition to brain, lung or skin. Serum was collected and subjiected to ctDNA extraction. ctDNA were then treated by methylation-sensive bisulfite and sequencing.

2021-12-23 | GSE163763 | GEO

Longitudinal analysis of personal cfDNA methylome patterns in metastatic prostate cancer [plasma]

Project description:Disease progression and therapeutic resistance are hallmarks of advanced stage prostate cancer (PCa), which remains a major cause of cancer-related mortality around the world. Longitudinal studies, coupled with the use of liquid biopsies, offer a potentially new and minimally invasive platform to study the dynamics of tumour progression. Our study aimed to investigate the dynamics of personal methylomic profiles of metastatic PCa (mPCa) patients, during disease progression and therapy administration. 52 plasma samples from 9 patients with mPCa were collected, longitudinally, over 13-21 months. After cell-free DNA (cfDNA) isolation, DNA methylation was profiled using the Infinium MethylationEPIC BeadChip and analysed using the minfi software. The top 5% most variable probes across time, within each individual, were utilised to study dynamic methylation patterns during disease progression and therapeutic response. Statistical testing was carried out to identify and validate ctDNA differentially methylated genes (DMGs). Personal cfDNA global methylation patterns were temporally stable throughout disease course. A proportion of analysed CpG sites presented a dynamic temporal pattern that was consistent with clinical events, such as therapy administration, and were prominently associated with immune response pathways. Study of ctDNA identified >2,000 DMGs with dynamic methylation patterns. We concluded that longitudinal assessment of cfDNA methylation in mPCa patients unveiled dynamic patterns associated with the occurrence of specific clinical events, thus highlighting the potential of using liquid biopsies to study PCa progression.

2021-09-01 | GSE157273 | GEO

Reliable tumor detection using cerebrospinal fluid cell-free DNA methylomes in pediatric medulloblastoma

Project description:Medulloblastoma (MB) is an embryonal tumor of the cerebellum and a highly malignant childhood brain tumor. Cell-free circulating tumor DNA (ctDNA) from the cerebrospinal fluid (CSF) of patients with brain tumors faithfully represent genomic alterations of brain tumors. Distinct epigenetic signatures among subgroups of MB allow us to detect epigenetic alterations in CSF to aid classify and guide therapy of MB tumors. Here, we evaluate DNA methylation and hydroxymethylation of ctDNA derived from small amount of CSF (200 µL) and matched tumor DNA from 3 MB patients. We find highly concordance of DNA methylation and hydroxymethylation between CSF ctDNA and tumor DNA, especially in CpG islands. Importantly, CSF ctDNA can mostly recapitulate the dynamic changes of DNA methylation and hydroxymehtylation in tumor species compared to healthy cerebellums. Those MB tumor signature CpGs’ DNA methylation status are recovered in CSF ctDNA can clearly distinguish MB subgroups by utilizing public large cohort data. We further identified potential diagnostic and prognostic DNA methylation markers in CSF ctDNA. Our results show that CSF ctNDA methylation and hydroxymethylation can be a minimal invasive method to assess epigenetic alterations of MB, which is complementary to current diagnoses of MB tumors.

2020-10-28 | GSE142241 | GEO

Trajectories of maternal epigenetic aging measures across pregnancy and postpartum

Project description:Pregnancy has been proposed as a biological “stress test” that may transiently accelerate maternal biological aging, followed by partial recovery in the postpartum period; however, longitudinal evidence characterizing these trajectories remains limited. This longitudinal study followed 130 women across mid to late pregnancy, early postpartum (6–9 months), and later postpartum (36–43 months) to characterize nonlinear changes in multiple markers of biological aging. Biological aging was assessed using complementary indicators, including telomere length, DNA methylation–based epigenetic aging measures, and pace-of-aging metrics. Genome-wide DNA methylation data were generated from maternal biospecimens using the Illumina Infinium MethylationEPIC v2.0 BeadChip to support derivation of epigenetic aging measures and evaluation of longitudinal methylation dynamics. Generalized additive mixed models were used to examine within-person changes over time. Results indicated relative stability or slowing of biological aging during early postpartum, followed by marker-specific patterns of stabilization or decline during later postpartum. Subsequent pregnancy during the later postpartum period was associated with shorter telomere length and altered recovery trajectories, including accelerated pace of aging among women who became pregnant again. Together, these findings suggest that while partial recovery of biological aging markers may occur following pregnancy, such recovery may be sensitive to additional reproductive demands. The DNA methylation data deposited here support longitudinal analyses of maternal biological aging across pregnancy and postpartum and provide a resource for future studies examining reproductive influences on epigenetic aging processes. Additional study data available via figshare at: https://doi.org/10.6084/m9.figshare.30005287

2026-05-04 | GSE318189 | GEO

Application of Polygenic Methylation Markers in Postoperative Recurrence Monitoring of Colorectal Cancer

Project description:This study dynamically monitored the prognosis of stage I-IV colorectal cancer patients who could receive radical surgical resection by detecting the levels of polygene methylation in plasma samples from patients with colorectal cancer. In patients with colorectal cancer feasible radical surgery, plasma ctDNA methylation detection was performed before and after surgical treatment and during regular follow-up to explore the predictive effect of plasma ctDNA methylation status at different time points on postoperative recurrence. To explore whether postoperative dynamic monitoring of plasma ctDNA methylation can be used for adjuvant chemotherapy efficacy evaluation and whether it can indicate tumor recurrence and metastasis earlier than imaging examination.

| 2739915 | ecrin-mdr-crc