Tissue-specific cell-free DNA degradation quantifies circulating tumor DNA burden

Abstract

Profiling of circulating tumor DNA (ctDNA) may offer a non-invasive approach to monitor disease progression. Here, we develop a quantitative method, exploiting local tissue-specific cell-free DNA (cfDNA) degradation patterns, that accurately estimates ctDNA burden independent of genomic aberrations. Nucleosome-dependent cfDNA degradation at promoters and first exon-intron junctions is strongly associated with differential transcriptional activity in tumors and blood. A quantitative model, based on just 6 regulatory regions, could accurately predict ctDNA levels in colorectal cancer patients. Strikingly, a model restricted to blood-specific regulatory regions could predict ctDNA levels across both colorectal and breast cancer patients. Using compact targeted sequencing (<25 kb) of predictive regions, we demonstrate how the approach could enable quantitative low-cost tracking of ctDNA dynamics and disease progression.

Comprehensive Approach to Distinguish Patients with Solid Tumors from Healthy Controls by Combining Androgen Receptor Mutation p.H875Y with Cell-Free DNA Methylation and Circulating miRNAs

“…The cfDNA profile of a cancer patient differs from a healthy individual, whereby it consists of fragments originating from tumor cells, also called circulating tumor DNA (ctDNA). Additionally, these DNA fragments have a specific footprint indicating the tissue of origin [ 38 ]. Although we did not estimate the percentage of ctDNA of the total plasma cfDNA, we detected a higher mutational burden in cancer patients compared to healthy individuals.…”

Quantitative Analysis of Plasma Cell-Free DNA and Its DNA Integrity and Hypomethylation Status as Biomarkers for Tumor Burden and Disease Progression in Patients with Metastatic Neuroendocrine Neoplasias

“…cfDNA can be detected at a low concentration in many body fluids, including plasma, where it has been shown to have a short half-life of less than 2.5 h. In healthy individuals, the majority of circulating plasma cfDNA is derived from hematopoietic cells, especially after intense exercise [ 6 ]. Elevated cfDNA plasma concentrations correlating with tumor burden and poor prognosis have been reported for many metastatic cancers [ 9 , 10 , 11 ]. Although the exact mechanism remains to be clarified, the high degree of necrosis in many advanced tumors and the release of tumor DNA fragments via phagocytosis of necrotic neoplastic cells might contribute to the increased release of cell-free tumor DNA into the circulation.…”

The Role of Dielectrophoresis for Cancer Diagnosis and Prognosis

“…There is increasing evidence of the intra-tumor heterogeneity in cancer due to spatial [ 97 ] and temporal heterogeneity [ 98 ], with a plethora of sub-clonal mutations, carried only by a fraction of the tumor cells [ 99 ]. For this reason, liquid biopsy, based on the detection in the bloodstream of circulating tumor DNA (ctDNA, tumor-derived fragmented DNA not associated with cells) and broader circulating free DNA (cfDNA, degraded DNA fragments released by apoptotic cells and necrotic cells, not necessarily of tumor origin) are emerging means for a non-invasive investigation of the tumor molecular structure [ 100 , 101 ].…”

“…Next-generation sequencing (NGS) can identify mutations even with a low representation (up to 3%) by means of very high coverage sequencing, but additional bioinformatics and machine learning tools are required to identify clinically relevant mutations in a background of errors, noise, and random mutations [ 102 ], challenging the contribution of passenger mutations that can still be used to improve cancer subclassification [ 101 , 103 ]. Because of genome plasticity, cfDNA might not be fully informed of cancer evolution, representing an average of multiple subclones present in the individual patient, providing the rationale for the search for alternative non-invasive and not-expensive platforms.…”