Liquid footprinting: A novel approach for DNA footprinting using short double-stranded cell-free DNA from plasma
The diagnostic potential of short double-stranded cell-free DNA in blood plasma has not been recognized, yet. Here, we present a method for enrichment of short double-stranded cell-free DNA with an average length of about 40 base pairs out of whole plasma cfDNA for high-throughput DNA sequencing. This class of cell-free DNA is enriched at gene promoters, binding sites of transcription factors as well as structural DNA-binding proteins thus facilitating a genome-wide DNA footprint in liquid biopsies. In short double-stranded cell-free DNA from healthy individuals, we found a significant enrichment of 203 different transcription factor consensus motifs. Additionally, levels of short double-stranded cell-free DNA significantly correlates with DNA-methylation and H3K4me3 histone modification levels, as well as transcription at specific genomic regions. When comparing pancreatic ductal adenocarcinoma with colorectal carcinoma or septic with post-operative control patient samples, we identified 731 and 1107 differential occupied loci, respectively. Using these differential regions, different disease types can be clearly distinguished by principal component analysis showing the diagnostic potential of this new class of biomarkers in liquid biopsies.