87: Tracing Allograft Injury with cfDNA Methylation

Nature Communications - This study used fragment-level, sequence-based DNA methylation of circulating cell-free DNA to map cellular origins of tissue damage after liver transplant. An expanded methylation atlas of liver cell types and hybridization capture bisulfite sequencing of 130 serum samples from 44 patients showed that sustained hepatocyte and biliary epithelial cfDNA within the first month signals early allograft injury and that cfDNA composition distinguishes hepatocellular versus biliary etiologies. Key terms: cell-free DNA, DNA methylation, liver transplant, allograft injury, hepatocyte. Study Highlights:The authors generated an expanded liver cell-type methylation atlas from 476 methylomes and used hybridization capture bisulfite sequencing on 130 serum samples from 44 transplant patients. Post-reperfusion cfDNA concentrations rose ~5-fold driven mainly by hepatocyte, stellate and endothelial contributions, and hepatocyte cfDNA correlated with AST/ALT. Patients without allograft injury showed recovery of liver-derived cfDNA within the first week, whereas sustained hepatocyte and biliary epithelial cfDNA from POD7–POD30 indicated early allograft injury. CfDNA composition at biopsy timepoints discriminated hepatocellular, biliary, and mixed injury phenotypes. Conclusion:Cell-free methylated DNA in circulation can indicate allograft injury and discriminate amongst causes of allograft injury matching tissue-biopsy-proven diagnosis. Music:Enjoy the music based on this article at the end of the episode. Article title:Circulating cell-free DNA methylation patterns indicate cellular sources of allograftinjury after liver transplant Journal:Nature Communications DOI:10.1038/s41467-025-60507-9 Reference:https://doi.org/10.1038/s41467-025-60507-9 License:This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support:Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 Official website https://basebybase.com On PaperCast Base by Base you'll discover the latest in genomics, functional genomics, structural genomics, and proteomics. Episode link: https://basebybase.com/episodes/cfdna-methylation-liver-transplant QC:This episode was checked against the original article PDF and publication metadata for the episode release published on 2025-07-26. QC Scope:- article metadata and core scientific claims from the narration- excludes analogies, intro/outro, and music- transcript coverage: Audited the main sections describing: the cfDNA methylation atlas expansion, the fragment-level deconvolution method, peri- and post-transplant cfDNA dynamics, differentiation of hepatocellular vs biliary injury, extra-hepatic cfDNA signals, and clinical translation/validation discussion.- transcript topics: Expansion of liver cell-type DNA methylation atlas; Fragment-level deconvolution of cfDNA; Post-transplant cfDNA dynamics and tissue origins; Differentiation of hepatocellular vs biliary injury; Extrahepatic cfDNA signals (neuronal, cardiac, renal); Clinical implications, limitations, and validation needs QC Summary:- factual score: 10/10- metadata score: 10/10- supported core claims: 5- claims flagged for review: 0- metadata checks passed: 4- metadata issues found: 0 Metadata Audited:- article_doi- article_title- article_journal- license Factual Items Audited:- DOI matches the canonical DOI 10.1038/s41467-025-60507-9- Article title matches canonical title (formatting variants allowed)- Journal matches Nature Communications- License matches CC BY 4.0 variant QC result: Pass.