Project description:Cell-free DNA circulates in blood bound to nucleosomes, forming cell-free chromatin (cfChromatin) that retains epigenetic features, including nucleosome positioning and histone modifications. cfChromatin provides a rich source of cancer biomarkers; however, low abundance of tumor-derived cfChromatin and limited availability of clinical samples pose challenges for liquid biopsy research. To address this, we developed a framework to simulate cfChromatin nucleosomal distributions using nuclease-treated conditioned media from tissue cultures. Whole-genome sequencing confirmed that inferred nucleosome positioning reflected cell-type-specific gene expression and chromatin accessibility patterns, and comparisons with plasma cfChromatin from xenografted mice revealed concordant nucleosome profiles. Notably, simulated cfChromatin displayed stronger tumor-specific nucleosome profiles than patient plasma, where hematopoietic-derived cfChromatin dilutes signal. We further leveraged simulated cfChromatin to advance cell-free chromatin immunoprecipitation and sequencing methods, identifying repressive and bivalent chromatin domains predictive of transcriptional activity. Altogether, our results demonstrate utility of simulated cfChromatin as a scalable preclinical tool for liquid biopsy research.

2025-10-01 | GSE294649 | GEO

Cell-Free Plasma MicroRNAs that Identify Patients with Glioblastoma

Project description:Cell-Free Plasma MicroRNAs that Identify Patients with Glioblastoma

| PRJNA764727 | ENA

Repeat-element-aware profiling of plasma cell-free RNA

Project description:Repeat-element-aware profiling of plasma cell-free RNA

| PRJNA562932 | ENA

Fragmentomic features of seminal plasma cell-free DNA revealed by low-coverage whole-genome sequencing in male infertility

Project description:Seminal plasma cell-free DNA

| PRJEB98078 | ENA

Plasma Cell-free RNA Signatures of Inflammatory Syndromes in Children

Project description:Plasma Cell-free RNA Signatures of Inflammatory Syndromes in Children