Detection of Cell Types Contributing to Cancer From Circulating, Cell-Free Methylated DNA

Abstract

Detection of cellular changes in tissue biopsies has been the basis for cancer diagnostics. However, tissue biopsies are invasive and limited by inaccuracies due to sampling locations, restricted sampling frequency, and poor representation of tissue heterogeneity. Liquid biopsies are emerging as a complementary approach to traditional tissue biopsies to detect dynamic changes in specific cell populations. Cell-free DNA (cfDNA) fragments released into the circulation from dying cells can be traced back to the tissues and cell types they originated from using DNA methylation, an epigenetic regulatory mechanism that is highly cell-type specific. Decoding changes in the cellular origins of cfDNA over time can reveal altered host tissue homeostasis due to local cancer invasion and metastatic spread to distant organs as well as treatment responses. In addition to host-derived cfDNA, changes in cancer cells can be detected from cell-free, circulating tumor DNA (ctDNA) by monitoring DNA mutations carried by cancer cells. Here, we will discuss computational approaches to identify and validate robust biomarkers of changed tissue homeostasis using cell-free, methylated DNA in the circulation. We highlight studies performing genome-wide profiling of cfDNA methylation and those that combine genetic and epigenetic markers to further identify cell-type specific signatures. Finally, we discuss opportunities and current limitations of these approaches for implementation in clinical oncology.

Circulating Tumor DNA as a Cancer Biomarker: An Overview of Biological Features and Factors That may Impact on ctDNA Analysis

“…Matching the epigenetic footprint of these ctDNA fragments against reference databases would enable the molecular classification of cancers of unknown origin. In line with these data, the stability of DNA methylation and the presence of cell-specific methylation patterns can also contribute to the identification of tumor origin or even the detection of metastasis through cfDNA analysis ( 55 ). Specifically, the analysis of differentially methylated regions in colon and liver tissues enabled the differentiation of patients with liver or colon cancer but also, the discrimination between colon cancer patients with and without liver metastasis ( 56 ).…”

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

“…For these algorithms to perform well, high quality methylation atlases [ 32 , 34 ] based on samples comprising of preferably one cell type are required to select appropriate markers/loci that are robust enough to differentiate between distinct cell types in a mixture of unknown cell types. There is currently a trend towards broader sequencing techniques called ‘third generation liquid biopsy’ [ 87 , 88 ]. Techniques such as WGBS lead to higher sensitivity by using many markers—also called “features”.…”

Circulating Tumor DNA-Based Genomic Profiling Assays in Adult Solid Tumors for Precision Oncology: Recent Advancements and Future Challenges

“…However, currently approved ctDNA CGP assays would not be able to identify the origin of the mutations (inter-or intratumoral heterogeneity) without previous knowledge of the tumor genomic profile. Future studies exploring the use of methylation and fragmentomic features of cfDNA may help identify their cellular origins [148,149]. The shorter TAT of cfDNA-based CGP also suggests that liquid biopsy would be more beneficial than tissue profiling for aggressive and fast progression cancers, allowing earlier treatment commencement [144].…”