Cell-Free DNA Fragmentomics: The Novel Promising Biomarker

Abstract

Cell-free DNA molecules are released into the plasma via apoptotic or necrotic events and active release mechanisms, which carry the genetic and epigenetic information of its origin tissues. However, cfDNA is the mixture of various cell fragments, and the efficient enrichment of cfDNA fragments with diagnostic value remains a great challenge for application in the clinical setting. Evidence from recent years shows that cfDNA fragmentomics’ characteristics differ in normal and diseased individuals without the need to distinguish the source of the cfDNA fragments, which makes it a promising novel biomarker. Moreover, cfDNA fragmentomics can identify tissue origins by inferring epigenetic information. Thus, further insights into the fragmentomics of plasma cfDNA shed light on the origin and fragmentation mechanisms of cfDNA during physiological and pathological processes in diseases and enhance our ability to take the advantage of plasma cfDNA as a molecular diagnostic tool. In this review, we focus on the cfDNA fragment characteristics and its potential application, such as fragment length, end motifs, jagged ends, preferred end coordinates, as well as nucleosome footprints, open chromatin region, and gene expression inferred by the cfDNA fragmentation pattern across the genome. Furthermore, we summarize the methods for deducing the tissue of origin by cfDNA fragmentomics.

Cancer Bioenergetics and Tumor Microenvironments—Enhancing Chemotherapeutics and Targeting Resistant Niches through Nanosystems

“…cfDNA shows a complex release pattern attributed to the interconnected cellular process and originating sources. Studies in eight different cancer cell lines and patients' plasma samples have elucidated the characteristics of cfDNA, confirming its release exclusively by cancer cells, with different release patterns [211][212][213][214][215][216]. Screening of the bioenergetics flux parameters showed a correlation between cfDNA release patterns and cellular origin, cancer status, and proliferation phase [217][218][219][220].…”

Plasma Circular RNAs as Biomarkers for Breast Cancer

“…There are several explanations for this phenomenon, e.g., the type of circRNA secretion in the blood. Indeed, plasma circRNAs can arise by passive cell death induced by drugs, hypoxia, inflammation, or endogenous molecular pathways, or they can also be actively secreted into the bloodstream packaged in EVs or TEPs [111]. This implies that the comparison of the circRNA profile of plasma and tissue depends on active/passive molecular secretion and tumor/tissue integrity.…”

The impact of preanalytical variables on the analysis of cell-free DNA from blood and urine samples

“…Subsequent research demonstrated elevated levels of cfDNA in patients with cancer ( Song et al, 2022 ; Wu et al, 2022 ) and inflammation ( Schneck et al, 2017 ), indicating that cfDNA analysis could be a valuable tool for health monitoring ( Hayashi et al, 2019 ). Originating from apoptotic or necrotic events and active release mechanisms in the presence of intracellular circulating nucleases ( Qi et al, 2023 ), cfDNA, with its modal size around 166 base pairs (bp) in plasma, has been linked to nucleosomal structures ( Lo et al, 2021 ). Due to the stability of cfDNA molecules in body fluids ( Polini et al, 2019 ), their wealth of genetic and epigenetic information ( Wu et al, 2019 ; Xiao et al, 2022 ), and the noninvasive or minimally invasive nature of body fluid collection for cfDNA analysis ( Ellervik and Vaught, 2015 ), cfDNA is considered an ideal biomarker for disease prevention, diagnosis, treatment, and prognosis ( Szilagyi et al, 2020 ).…”