Epigenetics, fragmentomics, and topology of cell-free DNA in liquid biopsies

YMD Lo, DSC Han, P Jiang, RWK Chiu - Science, 2021 - science.org
Science, 2021science.org
BACKGROUND Liquid biopsies that are based on analysis of cell-free DNA from plasma
offer diagnostic information that is otherwise accessible conventionally through invasive
biopsies. Noninvasive prenatal testing has been used globally for the screening of fetal
chromosomal aneuploidies and has led to a considerable reduction in invasive prenatal
testing, such as use of amniocentesis. Cancer liquid biopsies have been used for the
selection of targeted therapies and monitoring of disease progression. Liquid biopsies for …
BACKGROUND
Liquid biopsies that are based on analysis of cell-free DNA from plasma offer diagnostic information that is otherwise accessible conventionally through invasive biopsies. Noninvasive prenatal testing has been used globally for the screening of fetal chromosomal aneuploidies and has led to a considerable reduction in invasive prenatal testing, such as use of amniocentesis. Cancer liquid biopsies have been used for the selection of targeted therapies and monitoring of disease progression. Liquid biopsies for organ transplant patients have been used to monitor graft dysfunction. The first applications of liquid biopsies are based on the detection of genetic markers in cell-free DNA, such as sex differences, genetic polymorphisms, or mutations. By studying nongenetic features of cell-free DNA molecules—including DNA methylation, fragmentation, and topology—understanding of cell-free DNA biology has expanded the spectrum and utilities of liquid biopsies.
ADVANCES
Cell-free DNA in plasma consists of a mixture of fragmented DNA molecules released from various tissues within the body. Each cell-free DNA fragment bears molecular signatures of its cell of origin, such as DNA methylation status. The methylation profile of circulating fetal DNA in the mother’s plasma correlates with that of the placenta and has been exploited as a means to develop noninvasive fetus-specific biomarkers that are not dependent on fetal sex or genotype. Circulating tumor-derived DNA bear methylation states that resemble the tumor tissue and have enabled the development of tests for the screening and localization of cancer. The fragmentation of plasma DNA is related to the nucleosomal organization, chromatin structure, gene expression, and nuclease content of the tissue of origin, resulting in characteristic signatures in the form of fragment size, nucleotide motifs at the fragment ends, single-stranded jagged ends, and the genomic locations of the fragmentation endpoints. For mitochondrial DNA that is originally in a circular form, fragmentation will also change its topology into a linear form. By noting these features of cell-free DNA fragments, the anatomical site of pathology could potentially be deduced, providing additional information than just quantifying mitochondrial DNA without regard to its form. The study of such characteristics has also enhanced our understanding of the biology and generation of cell-free DNA. The roles of nucleases in plasma DNA biology, such as deoxyribonuclease 1–like-3, have been explored by using gene-deletion mouse models and confirmed in humans bearing nuclease gene mutations, with potential implications for the pathogenesis of autoimmune diseases.
OUTLOOK
The use of DNA methylation, fragmentomic, and topologic analyses of circulating DNA, either in a targeted fashion or in a genomewide manner, will be expected to impact clinical practice. Clinical specimens covering more disease entities will need to be investigated to identify tissue-specific and disease-relevant signatures. During the discovery phase, to better delineate these signatures, mining is performed on high volumes of DNA data pooled within and across samples by using customized bioinformatics algorithms. Once these putative sets of signatures have been identified, signature- and target-specific assays could be developed, and large-scale clinical trials will be needed to validate these approaches. One application is in the development of plasma DNA–based cancer screening. One advantage of these approaches is the potentially large number of markers that can be developed to differentiate cancer and noncancer cells and in the ability to …
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