Unlocking the Future of Cancer Diagnostics with Circulating Tumor DNA (ctDNA)
Advances in cancer research have brought us closer to understanding the complex biology of tumors. One particularly promising area is the study of circulating tumor DNA (ctDNA)—tiny cell-free DNA fragments shed by cancer cells into the bloodstream. Detecting and analyzing these fragments represents a transformative approach to diagnosing and monitoring cancer, with unparalleled accuracy and minimal invasiveness.
What is Circulating Cell-Free DNA?
While genomic DNA represents the entire DNA within a cell that contains stable, inherited genetic information, circulating cell-free DNA (cfDNA) refers to DNA fragments freely floating in the bloodstream. These fragments are byproducts of cellular processes such as apoptosis (cell death) and can be classified as follows:
- Total cfDNA: This refers to all cell-free DNA present in the bloodstream, regardless of its source. It includes DNA from normal cell turnover, tissue damage, immune responses, and other physiological or pathological conditions.
- Circulating tumor DNA (ctDNA): A specific subset of cfDNA, this consists of DNA fragments shed by cancer cells. ctDNA contains genetic mutations or alterations unique to tumors, making it a critical marker for cancer diagnostics and monitoring.
How are cfDNA levels regulated?
Blood levels of cfDNA are determined by the balance between DNA release and clearance.
cfDNA Release
Circulating cell-free DNA (cfDNA) is released into the bloodstream through various biological processes. These processes occur under both normal and pathological conditions and contribute to the overall pool of cfDNA in the body. Key mechanisms of cfDNA release include [1]:
- Cell Death:
- Apoptosis (programmed cell death) and necrosis (cell death due to injury) are the primary contributors to cfDNA release. As cells undergo these processes, their DNA is fragmented and released into the bloodstream.
- Other DNA Release Mechanisms:
- Oncosis: A prelethal pathway that leads to cell death, which is accompanied by cellular swelling, organelle swelling, blebbing, and increased membrane permeability [2].
- Pyroptosis: An inflammatory type of programmed cell death characterized by cell swelling and osmotic lysis that includes the release of fragmented DNA [3].
- Phagocytosis: The engulfment and digestion of apoptotic or necrotic cells by immune cells, contributing to DNA release.
- Active Secretion: Some cells actively secrete DNA into the extracellular space, contributing to the circulating cfDNA pool.
- Neutrophil Extracellular Traps (NETs): Neutrophils, in response to infection or inflammation, release DNA to form structures known as NETs, which trap and kill pathogens [4].
Elevated cfDNA levels can result from conditions such as cancer, pregnancy, inflammation, or infections. In cancer, the tumor cells contribute a higher proportion of cfDNA, specifically circulating tumor DNA (ctDNA), which contains tumor-specific genetic alterations.
cfDNA clearance
cfDNA has a short half-life, typically ranging from a few minutes to 1–2 hours. This short half-life is advantageous for dynamic, real-time monitoring of biological conditions, such as evaluating treatment responses or assessing tissue damage. The levels of cfDNA in the bloodstream are regulated by efficient clearance mechanisms. The key mechanisms for cfDNA clearance include [1]:
- Organs Involved in Clearance:
- Liver, spleen, and kidneys play a significant role in removing cfDNA from the bloodstream. In liver and spleen, DNA and nucleosomes are mainly trapped by tissue-specific macrophages, whereas extracellular single-stranded DNA is removed by the glomeruli of the kidneys.
- Circulating Enzymes:
- Enzymes such as DNase I are crucial for the degradation of cfDNA. These enzymes break down DNA into smaller fragments, ensuring that cfDNA does not accumulate in the bloodstream.
Impaired cfDNA Clearance
In healthy individuals, cfDNA is rapidly cleared from the circulation, maintaining relatively low levels. In pathological conditions like cancer, chronic inflammation, or certain infections, the clearance mechanisms may become overwhelmed or impaired, leading to an accumulation of cfDNA. For example:
- Cancer: Tumor growth, cell death, and inadequate clearance contribute to an increased presence of ctDNA in the bloodstream. As the tumor progresses, the proportion of cfDNA from the tumor (ctDNA) can rise significantly.
- Chronic Inflammation or Infections: Persistent cell death and immune activation can overwhelm the clearance systems, resulting in elevated cfDNA levels.
This accumulation of cfDNA, particularly ctDNA, serves as a distinctive feature that can be leveraged for diagnostics. The concentration and specific mutations present in cfDNA can provide valuable insights into tumor burden, treatment response, and disease progression.
Liqomics & Our Services
Liqomics offers LymphoVista, a ctDNA-based MRD test for lymphomas with extremely high sensitivity and specificity and MRD monitoring solutions for other cancers. Learn more about our services here, and get in touch to see what we can offer.
Outlook
Now that you have a solid understanding of cfDNA, stay tuned for our upcoming follow-up article, where we’ll explore the biological benefits of cfDNA and the applications of ctDNA in cancer detection and treatment monitoring.
Author: Lisa Baum, Bioinformatician and Data Scientist, Liqomics
Reference to the literature used
[1] Kustanovich A, Schwartz R, Peretz T, Grinshpun A. Life and death of circulating cell-free DNA. Cancer Biol Ther. 2019;20(8):1057-1067. doi: 10.1080/15384047.2019.1598759. Epub 2019 Apr 16. PMID: 30990132; PMCID: PMC6606043.
[2] Fink SL, Cookson BT. Apoptosis, pyroptosis, and necrosis: mechanistic description of dead and dying eukaryotic cells. Infect Immun. 2005 Apr;73(4):1907-16. doi: 10.1128/IAI.73.4.1907-1916.2005. PMID: 15784530; PMCID: PMC1087413.
[3] Liu Y, Pan R, Ouyang Y, Gu W, Xiao T, Yang H, Tang L, Wang H, Xiang B, Chen P. Pyroptosis in health and disease: mechanisms, regulation and clinical perspective. Signal Transduct Target Ther. 2024 Sep 20;9(1):245. doi: 10.1038/s41392-024-01958-2. PMID: 39300122; PMCID: PMC11413206.
[4] Rada B. Neutrophil Extracellular Traps. Methods Mol Biol. 2019;1982:517-528. doi: 10.1007/978-1-4939-9424-3_31. PMID: 31172493; PMCID: PMC6874304.
