Tracing the Origin of Cell-Free DNA Molecules through Tissue-Specific Epigenetic Signatures

Abstract

All cell and tissue types constantly release DNA fragments into human body fluids by various mechanisms including programmed cell death, accidental cell degradation and active extrusion. Particularly, cell-free DNA (cfDNA) in plasma or serum has been utilized for minimally invasive molecular diagnostics. Disease onset or pathological conditions that lead to increased cell death alter the contribution of different tissues to the total pool of cfDNA. Because cfDNA molecules retain cell-type specific epigenetic features, it is possible to infer tissue-of-origin from epigenetic characteristics. Recent research efforts demonstrated that analysis of, e.g. methylation patterns, nucleosome occupancy, and fragmentomics determined the cell- or tissue-of-origin of individual cfDNA molecules. This novel tissue-of origin-analysis enables to estimate the contributions of different tissues to the total cfDNA pool in body fluids and find tissues with increased cell death (pathologic condition), expanding the portfolio of liquid biopsies towards a wide range of pathologies and early diagnosis. In this review, we summarize the currently available tissue-of-origin approaches and point out the next steps towards clinical implementation.

Pre-Analytical Evaluation of Streck Cell-Free DNA Blood Collection Tubes for Liquid Profiling in Oncology

“…As such, temperature-controlled shipping is required. Second, the diagnostic sensitivity and specificity of ctDNA have been shown to be increased by parallel assessment of other biomarkers and other genomic features of ctDNA [ 36 , 37 , 38 ]; however, cfDNA BCTs were not designed, optimized, and tested for the analysis of auxiliary biomarkers such as DNA methylation patterns [ 39 ], proteins, or cell-free RNA [ 40 ]. Last, in order to reverse the chemical fixations in these tubes, the DNA extraction procedure requires an extended heating step [ 10 ].…”

Identification and functional analysis of circulating extrachromosomal circular DNA in schizophrenia implicate its negative effect on the disorder

“…Previous studies on circulating cfDNA have provided clues to answer some of the questions addressed. Tissue-speci c epigenetic markers carried by the cfDNA have been utilized for identi cation of the tissue-of-origins of cfDNA 24,74 . It would thus be convenient to investigate the tissue origins of circulating eccDNA by the strategy.…”

New Perspectives on the Importance of Cell-Free DNA Biology

“…This is especially important in the context of cancer screening, where the identification of the tissue-of-origin of underlying cancers is crucial. This is a challenging task, but in the next section we explore how this is becoming increasingly possible through rapid progress in mapping various tissue-of-origin classifiers in the genome and in cfDNA [ 170 , 171 ].…”

“…Pathology-related changes in transcriptional programs in specific cell types could be identified with this method. In another proof-of-principle study, immunoprecipitation of H3 lysine 36 trimethylation (H3K36me3)-modified nucleosomes, a histone modification associated with active gene transcription, was used as a liquid biopsy marker to identify tumor-specific transcriptional activity of mutated alleles in non-small cell lung cancer [ 171 , 183 ].…”