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Updated: Sep 11, 2025
A Standardized Liquid Biopsy Preanalytical Protocol for Downstream Circulating-Free DNA Applications
Published on: September 16, 2022
The circulating cell-free DNA landscape in sepsis is dominated by impaired liver clearance
Kiki Cano-Gamez1, Patrick Maclean2, Masato Inoue3
1Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Department of Clinical and Biomedical Sciences, University of Exeter, Exeter, UK.
Insights
Circulating cell-free DNA (cfDNA) significantly increases in sepsis, not from cell death, but impaired liver clearance. This cfDNA offers diagnostic potential for severe infections and critical illness.
Area of Science:
- Molecular Biology
- Genomics
- Critical Care Medicine
Background:
- Circulating cell-free DNA (cfDNA) shows promise as a biomarker.
- The role of cfDNA in severe infections like sepsis remains largely undefined.
Purpose of the Study:
- To investigate the dynamics and origins of cfDNA in sepsis patients.
- To explore the diagnostic potential of cfDNA in severe infections.
Main Methods:
- Profiling cfDNA from sepsis patients and healthy controls.
- Utilizing methylation-based deconvolution and fragmentation/end-motif analysis.
- Developing novel methods to quantify cfDNA nucleosome footprints and integrate with single-cell data.
Main Results:
- A 41-fold increase in cfDNA was observed in sepsis patients.
- Evidence suggests impaired hepatic clearance, not increased cell death, drives cfDNA accumulation.
- cfDNA nucleosome footprints indicate Kupffer cell and liver parenchyma activity, especially in liver dysfunction.
- Pathogen-derived cfDNA was detected, indicating diagnostic utility.
Conclusions:
- cfDNA accumulation in sepsis is linked to reduced clearance and prolonged nuclease exposure.
- cfDNA analysis provides insights into cellular activity and organ dysfunction.
- cfDNA holds significant potential for diagnosing sepsis and other critical illnesses.
Abstract:
Circulating cell-free DNA (cfDNA) is a promising molecular biomarker, but its role in severe infection is unclear. Here, we profile cfDNA from sepsis patients and controls, demonstrating a 41-fold increase during disease. Methylation-based deconvolution revealed similar cfDNA compositions in the two groups, suggesting that cfDNA accumulation during disease is due not to excess cell death but to impaired hepatic clearance. Fragmentation and end-motif patterns both support this hypothesis, suggesting prolonged exposure of cfDNA to circulating nucleases. In addition, we show that cfDNA retains nucleosome footprints informative of gene activity. By developing a novel method to quantify these footprints and integrate them with single-cell data, we report an increase in cfDNA from Kupffer cells and liver parenchyma in patients with liver dysfunction. Finally, we show that cfDNA contains pathogen-derived material, highlighting its diagnostic potential. This high-throughput, multimodal study provides a reference for understanding cfDNA's role in sepsis and critical illness.
