The Utility of Repetitive Cell-Free DNA in Cancer Liquid Biopsies

Abstract

Liquid biopsy is a broad term that refers to the testing of body fluids for biomarkers that correlate with a pathological condition. While a variety of body-fluid components (e.g., circulating tumor cells, extracellular vesicles, RNA, proteins, and metabolites) are studied as potential liquid biopsy biomarkers, cell-free DNA (cfDNA) has attracted the most attention in recent years. The total cfDNA population in a typical biospecimen represents an immensely rich source of biological and pathological information and has demonstrated significant potential as a versatile biomarker in oncology, non-invasive prenatal testing, and transplant monitoring. As a significant portion of cfDNA is composed of repeat DNA sequences and some families (e.g., pericentric satellites) were recently shown to be overrepresented in cfDNA populations vs their genomic abundance, it holds great potential for developing liquid biopsy-based biomarkers for the early detection and management of patients with cancer. By outlining research that employed cell-free repeat DNA sequences, in particular the ALU and LINE-1 elements, we highlight the clinical potential of the repeat-element content of cfDNA as an underappreciated marker in the cancer liquid biopsy repertoire.

Cancer relevance of circulating antibodies against LINE-1 antigens in humans

“…Extended testing validated this finding in patients with lung (NSCL, SCL), esophageal, ovarian, pancreatic, and liver cancers; other cancer types remain to be thoroughly analyzed. L1 desilencing was previously considered as a cancer biomarker detectable by hypomethylation in circulating cell-free DNA in liquid biopsies (Ardeljan et al, 2017;Gezer et al, 2022).…”

“…Extended testing validated this finding in patients with lung (NSCL, SCL), esophageal, ovarian, pancreatic, and liver cancers; other cancer types remain to be thoroughly analyzed. L1 desilencing was previously considered as a cancer biomarker detectable by hypomethylation in circulating cell-free DNA in liquid biopsies (Ardeljan et al, 2017; Gezer et al, 2022). Here, we demonstrate that the epigenetic dysregulation of L1 can generate an additional type of biomarker – circulating autoantibodies against L1 antigens – that can be detected by a simple and robust blood test.…”

New Perspectives on the Importance of Cell-Free DNA Biology

“…Significant research efforts in the last decade uncovered a rich landscape of cfDNA physico-chemical features (reviewed in [ 130 , 137 , 138 , 139 , 140 ]). Beyond hotspot mutations, numerous cfDNA features are candidate biomarkers, including (i) various genetic features, such as DNA sequence features ( Figure 4 A), chromosomal abnormalities ( Figure 4 B), and topological forms ( Figure 4 C); (ii) primary epigenetic markers such as DNA methylation ( Figure 4 D) and histone modifications ( Figure 4 E); and (iii) various secondary epigenetic features that cfDNA molecules attain intracellularly or extracellularly following disruption of the primary structure of DNA, such as binding to proteins, extracellular vesicles, or cell membranes ( Figure 4 F), and fragmentomic features ( Figure 4 G).…”

“…It is not yet clear how cfDNA fragments are integrated into host genomes, but some evidence suggests that it may occur through the non-homologous end-joining (NHEJ) double-strand DNA-repair pathway [ 113 , 364 , 377 ]. Alternatively, ctDNA enriched in specific retrotransposons (e.g., a hot LINE-1 element) [ 139 , 378 , 379 ] could, by virtue of their inherent mobility, penetrate recipient cells and initiate tumor formation upon “cut-and-paste” insertion into host tumor suppressor genes [ 380 , 381 ]. While there is no direct evidence, it is interesting to speculate here on the possibility of lateral transfer of therapy resistance mutations from resistant cells to surrounding cells.…”

The Clinical Utility of Droplet Digital PCR for Profiling Circulating Tumor DNA in Breast Cancer Patients

“…Furthermore, the detection of circulating nucleic acids—comprised of segments of genomic DNA and various RNA types, such mRNA and noncoding RNAs—in serum or plasma is increasingly regarded as a potential biomarker in oncology [ 12 ]. Although many types of nucleic acids are present in bodily fluids, cell-free DNA (cfDNA) has to date received the most research attention and has demonstrated significant potential as a highly sensitive and specific biomarker for the management of numerous cancer types across all disease stages and phases of cancer management [ 13 ]. Although cfDNA is present in many types of bodily fluids, such as serum, plasma, urine, pleural fluid, cerebrospinal fluid, and saliva [ 14 , 15 , 16 , 17 ], blood (plasma and serum) represents the most extensively characterized source of cfDNA.…”