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Circulating, cell-free methylated DNA reveals cellular sources of allograft injury after liver transplant (LTR cell-free DNA)

ABSTRACT: Circulating, cell-free methylated DNA reveals cellular sources of allograft injury after liver transplant (LTR cell-free DNA)

PROVIDER: PRJNA1090946 | ENA |

REPOSITORIES: ENA

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Circulating, cell-free methylated DNA reveals cellular sources of allograft injury after liver transplant (LTR reference cell type)

Project description:Circulating, cell-free methylated DNA reveals cellular sources of allograft injury after liver transplant (LTR reference cell type)

| PRJNA1090947 | ENA

Circulating, cell-free methylated DNA reveals cellular sources of allograft injury after liver transplant (LTR cell-free DNA)

Project description:Molecular biomarkers to monitor changes after liver transplant are essential to reveal mechanisms of injury, guide clinical decision-making and improve patient outcomes. Current approaches have limited scope and are unable to differentiate between host and graft amongst the causes of graft injury. Here, we utilize circulating, cell-free methylated DNA released from dying cells to monitor cellular damages after liver transplant impacting the graft tissue as well as host organs. We expand existing cell-type-specific DNA methylation atlases curated from whole-genome bisulfite sequencing (WGBS) of healthy tissues to characterize liver cell-types relevant to injury progression and tissue repair. Liver cell-type-specific methylation blocks are validated through multi-omic data integration and found to be enriched in open chromatin and regulatory regions functionally important for the respective cell populations. Cell-free DNA (cfDNA) fragments were captured from patient serum by hybridization to CpG-rich DNA panels and mapped to the expanded DNA methylation atlases to inform tissue origins of cell types. We profiled 135 blood samples collected from 44 liver transplant patients at serial time points before and after transplant. We found that liver transplant initially results in multi-tissue cellular damage that subsequently recovers in patients with graft acceptance during the first post-operative week. Further, we show that sustained elevation of hepatocyte and biliary epithelial cfDNA beyond the first week is indicative of early-onset graft injury. Most notably, cfDNA composition can differentiate amongst causes of graft injury. Thus, cell-free methylated DNA can detect cellular damages and prompt early intervention.

2025-03-02 | GSE262273 | GEO

Circulating, cell-free methylated DNA reveals cellular sources of allograft injury after liver transplant (LTR reference cell type)

2025-03-02 | GSE262274 | GEO

Circulating, cell-free methylated DNA reveals cellular sources of allograft injury after liver transplant

Project description:Circulating, cell-free methylated DNA reveals cellular sources of allograft injury after liver transplant

| PRJNA1100632 | ENA

Circulating, cell-free methylated DNA reveals cellular sources of allograft injury after liver transplant

Project description:Circulating, cell-free methylated DNA reveals cellular sources of allograft injury after liver transplant

| PRJNA1090942 | ENA

Circulating, cell-free methylated DNA reveals cellular sources of allograft injury after liver transplant

Project description:Circulating, cell-free methylated DNA reveals cellular sources of allograft injury after liver transplant

| PRJNA1100631 | ENA

Circulating, cell-free methylated DNA reveals cellular sources of allograft injury after liver transplant [Reference Celltype Chromatin]

2025-03-02 | GSE263243 | GEO

Circulating, cell-free methylated DNA reveals cellular sources of allograft injury after liver transplant [Reference Celltype Chromatin]

Project description:Circulating, cell-free methylated DNA reveals cellular sources of allograft injury after liver transplant [Reference Celltype Chromatin]

| PRJNA1096335 | ENA

Circulating, cell-free methylated DNA reveals cellular sources of allograft injury after liver transplant

Project description:This SuperSeries is composed of the SubSeries listed below.

2025-03-02 | GSE262275 | GEO

DNA sequencing of Arabidopsis thaliana nrpd1-3 background with novel insertions of LTR retrotransposon ONSEN/COPIA78.

Project description:The intent of the experiment was to infer, from re-sequencing of genomic DNA, the coordinates of neo-insertions from activated ONSEN/COPIA78 LTR retrotrasnposon in Arabidopsis thaliana. For this, we performed Illumina 75 bp pair-end PCR-free DNA genome re-sequencing in several independent lines of RdDM mutant nrpd1-3.

2018-03-18 | E-MTAB-5883 | biostudies-arrayexpress

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