Human in vivo footprints from blood plasma samples for improved diagnostics in septic patients

BackgroundLiquid biopsy based on cell-free DNA (cfDNA) is an established approach in clinical diagnostics. In recent years, a fraction of cfDNA comprising short fragments has been discovered, that is enriched at gene promoters and binding sites of DNA-binding proteins. However, the diagnostic potential of such short double-stranded cell-free DNA (footprint DNA) remains to be fully explored. Therefore, we characterized the clinical utility of footprint DNA in septic patients. MethodsWe enriched for footprint DNA based on size selection and subsequent high-throughput DNA sequencing to receive an unbiased, genome-wide picture of the host response to the infection. Footprint DNA occupancies were analyzed for correlation with clinical metrics including urea, hemoglobin, or alanine aminotransferase (ALT). Additionally, footprint DNA markers were benchmarked by read and receiver operating curve (ROC) analysis against procalcitonin (PCT) as an established marker for infection status as well as against clinical parameters for early death prediction. FindingsWe found that levels of occupancy of footprint DNA at defined genomic loci semi-quantitatively correlated with physiological markers like ALT or urea from major organ systems including liver or kidney. In a small proof-of-concept cohort, differential signatures of DNA footprints distinguished between patient groups with bacterial and viral infections with an area under the ROC (AUROC) of 1.0, which is considerably better than PCT with an AUROC of 0.75. Likewise, footprint DNA could also predict early death in septic patients with an AUROC of 0.983, compared to the SOFA (Sepsis-related organ failure assessment) score with an AUROC of 0.76. InterpretationOur findings show that footprint DNA delivers quantitative information on physiology at the DNA level, demonstrating its diagnostic and prognostic potential. Identified footprint biomarker regions could be helpful in the clinical assessment of septic patients and other complex diseases outperforming current state-of-the-art clinical diagnostics. FundingThis study was financed with internal funds from Fraunhofer society.