A simple blood test may soon provide patients who have undergone liver transplants and their physicians with an early warning system capable of pinpointing liver allograft injury with unprecedented precision.
Researchers developed a noninvasive method that analyzes methylation patterns in cell-free DNA (cfDNA) to detect signs of liver allograft injury. The test detected damage and identified which specific liver cells were affected—offering physicians a clearer view of the transplant's condition long before the emergence of symptoms.
In the study, published in Nature Communications in 2025, researchers followed 44 liver transplant patients, collecting 130 blood samples before and after surgery. The breakdown included 28 patients for serial sampling (100 samples) and an additional 16 patients at biopsy time (30 samples). Using a specialized DNA methylation atlas covering 476 methylomes from more than 40 cell types, including key liver subtypes, the researchers traced cfDNA fragments back to their cellular origins. Whether hepatocytes or biliary epithelial cells were undergoing stress or damage, the signals appeared in the blood with remarkable specificity.
Conventional biomarkers like liver function tests often miss early signs of complications and don't differentiate between injury types. Tissue biopsy, while accurate, is invasive and typically reserved for symptomatic cases, as it remains the gold standard despite its limitations.
To improve detection, the researchers created a DNA methylation atlas covering 476 methylomes from more than 40 cell types, including liver-specific subtypes. This allowed them to trace cfDNA in blood samples to its cellular origin using unique methylation signatures.
Post-transplant, cfDNA levels rose 5-fold across all patients, reflecting increased liver cell turnover. Hepatocyte-derived cfDNA levels strongly correlated with AST and ALT enzymes (r = 0.81 and r = 0.82, respectively), supporting the method's reliability.
All 11 patients who later developed liver allograft injury had persistently elevated hepatocyte and biliary epithelial cfDNA during the first month. These signals appeared a median of 63 days (range, 2-203 days) before biopsy-confirmed diagnosis.
In contrast, patients without injury showed a return to baseline cfDNA levels within one week, suggesting cfDNA profiles may serve as early indicators of complications.
The method also differentiated injury types. Among 24 patients with biopsy-confirmed injury, cfDNA composition varied by pattern: hepatocyte cfDNA was higher in hepatocellular injury, whereas biliary cfDNA was elevated in biliary and mixed forms.
Changes in cfDNA profiles also revealed signs of injury beyond the liver, including increased neuron and kidney epithelial DNA. These findings may reflect surgical stress, anesthesia effects, or conditions like acute kidney injury or infection.
Unlike donor-derived cfDNA methods, which only confirm the presence of injury, this approach identified the injured cell type without requiring donor genotyping. This addresses a significant clinical need, as current noninvasive biomarkers have limited scope and fail to identify cellular causes of allograft injury.
The researchers noted that cfDNA methylation profiling could complement or reduce the need for liver biopsies, particularly in monitoring biliary complications, which are common but difficult to detect noninvasively.
Larger studies will be needed to confirm these findings and guide clinical integration. Nonetheless, the results suggest that cfDNA methylation analysis could be a promising, noninvasive tool for personalized, cell-specific monitoring after liver transplantation.
Full disclosures can be found in the published study.
Source: Nature Communications
