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.

Keywords: cell-free DNA; epigenetics; liquid biopsy; tissue-of-origin.

Figure 1

Tissue-of-origin analysis of cell-free DNA. (a) Different organs and various cell types release cell-free DNA (cfDNA) into blood plasma. (b) This clinical biospecimen represents a highly heterogeneous mixture of cfDNA molecules, often complicating the analytical differentiation between different cfDNA subtypes. (c) Multiple different epigenetic characteristics can be employed for tissue-of-origin analysis such as unique methylation patterns, fragmentation profiles and fragment end-points, transcription-factor binding sites occupancy, nucleosome positioning, as well as post-translational histone modifications. (d) Analysis of these features poses an analytical challenge, but various approaches developed recently enable determination of tissue-of-origin of individual cfDNA molecules, facilitating localization of tumors or tissue damage in specific regions such as the heart or liver.