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Updated: Aug 4, 2025
A Standardized Liquid Biopsy Preanalytical Protocol for Downstream Circulating-Free DNA Applications
Published on: September 16, 2022
Epigenetic liquid biopsies: a novel putative biomarker in immunology and inflammation
Ilana Fox-Fisher1, Ruth Shemer1, Yuval Dor1
1Department of Developmental Biology and Cancer Research, The Institute for Medical Research, Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel.
Insights
Liquid biopsies using cell-free DNA (cfDNA) offer a novel way to study immune cell dynamics. Analyzing cfDNA epigenetics reveals insights into immune cell turnover and diseases like cancer and autoimmune conditions.
Area of Science:
- Immunology
- Genomics
- Biomarker Discovery
Background:
- Tissue-level immune and inflammatory processes are difficult to detect using current methods.
- Standard blood tests, biomarkers, and imaging often fail to capture these subtle dynamics, creating a significant unmet need in biomedical research.
Purpose of the Study:
- To explore the potential of liquid biopsies for understanding human immune system dynamics.
- To propose the analysis of epigenetic features in immune cell-derived cell-free DNA (cfDNA) as a method to study immune cell turnover and disease states.
Main Methods:
- Analysis of nucleosome-size fragments of cell-free DNA (cfDNA) in blood.
- Examination of epigenetic information within cfDNA, including methylation patterns, fragmentation, and histone mark patterns.
- Inference of cfDNA cell of origin and pre-cell death gene expression.
Main Results:
- Cell-free DNA (cfDNA) contains rich epigenetic information, including methylation, fragmentation, and histone marks.
- This epigenetic data allows for the inference of cfDNA cell of origin and gene expression patterns prior to cell death.
- Immune cell-derived cfDNA holds potential for revealing immune cell turnover dynamics.
Conclusions:
- Liquid biopsies, through cfDNA epigenetic analysis, can broadly inform human immune system dynamics.
- This approach can aid in the study and diagnosis of various conditions, including cancer, inflammation, infectious diseases, autoimmune diseases, and vaccine responses.
- Epigenetic profiling of cfDNA presents a promising avenue for non-invasive monitoring of immune health and disease.
Abstract:
Immune and inflammatory processes occurring within tissues are often undetectable by blood cell counts, standard circulating biomarkers, or imaging, representing an unmet biomedical need. Here, we outline recent advances indicating that liquid biopsies can broadly inform human immune system dynamics. Nucleosome-size fragments of cell-free DNA (cfDNA) released from dying cells into blood contain rich epigenetic information such as methylation, fragmentation, and histone mark patterns. This information allows to infer the cfDNA cell of origin, as well as pre-cell death gene expression patterns. We propose that the analysis of epigenetic features of immune cell-derived cfDNA can shed light on immune cell turnover dynamics in healthy people, and inform the study and diagnosis of cancer, local inflammation, infectious or autoimmune diseases, as well as responses to vaccination.
