Circulating free DNA

Circulating free DNA (cfDNA) (also known as cell-free DNA) are degraded DNA fragments released to body fluids such as blood plasma, urine, cerebrospinal fluid, etc. Typical sizes of cfDNA fragments reflect chromatosome particles (~165bp), as well as multiples of nucleosomes, which protect DNA from digestion by apoptotic nucleases.[1] The term cfDNA can be used to describe various forms of DNA freely circulating in body fluids, including circulating tumor DNA (ctDNA), cell-free mitochondrial DNA (ccf mtDNA), cell-free fetal DNA (cffDNA) and donor-derived cell-free DNA (dd-cfDNA).[2] Elevated levels of cfDNA are observed in cancer, especially in advanced disease.[3] There is evidence that cfDNA becomes increasingly frequent in circulation with the onset of age.[4] cfDNA has been shown to be a useful biomarker for a multitude of ailments other than cancer and fetal medicine. This includes but is not limited to trauma, sepsis, aseptic inflammation, myocardial infarction, stroke, transplantation, diabetes, and sickle cell disease.[5] cfDNA is mostly a double-stranded extracellular molecule of DNA, consisting of small fragments (50 to 200 bp) [6][7] and larger fragments (21 kb) [8] and has been recognized as an accurate marker for the diagnosis of prostate cancer and breast cancer.[9]

Recent studies have laid the foundation for inferring gene expression from cell-free DNA, with EPIC-seq emerging as a notable advancement.[10] This method has substantially raised the bar for the noninvasive inference of expression levels of individual genes, thereby augmenting the assay's applicability in disease characterization, histological classification, and monitoring treatment efficacy.[10][11][12]

Other publications confirm the origin of cfDNA from carcinomas and cfDNA occurs in patients with advanced cancer. Cell‐free DNA (cfDNA) is present in the circulating plasma and in other body fluids.[13]

The release of cfDNA into the bloodstream appears by different reasons, including apoptosis, necrosis and NETosis. Its rapidly increased accumulation in blood during tumor development is caused by an excessive DNA release by apoptotic cells and necrotic cells. Active secretion within exosomes has been discussed, but it is still unknown whether this is a relevant or relatively minor source of cfDNA.[14]

cfDNA circulates predominantly as nucleosomes, which are nuclear complexes of histones and DNA.[15] cfDNA can also be observed in shorter size ranges (e.g. 50bp) and associated with regulatory elements. [16] They are frequently nonspecifically elevated in cancer but may be more specific for monitoring cytotoxic cancer therapy, mainly for the early estimation of therapy efficacy.[17]

  1. ^ Shtumpf M, Piroeva KV, Agrawal SP, Jacob DR, Teif VB (June 2022). "NucPosDB: a database of nucleosome positioning in vivo and nucleosomics of cell-free DNA". Chromosoma. 131 (1–2): 19–28. doi:10.1007/s00412-021-00766-9. PMC 8776978. PMID 35061087.
  2. ^ Dholakia S, De Vlaminck I, Khush KK (November 2020). "Adding Insult on Injury: Immunogenic Role for Donor-derived Cell-free DNA?". Transplantation. 104 (11): 2266–71. doi:10.1097/TP.0000000000003240. PMC 7590963. PMID 32217943.
  3. ^ Shaw JA, Stebbing J (January 2014). "Circulating free DNA in the management of breast cancer". Annals of Translational Medicine. 2 (1): 3. doi:10.3978/j.issn.2305-5839.2013.06.06. PMC 4200656. PMID 25332979.
  4. ^ Gravina S, Sedivy JM, Vijg J (June 2016). "The dark side of circulating nucleic acids". Aging Cell. 15 (3): 398–9. doi:10.1111/acel.12454. PMC 4854914. PMID 26910468.
  5. ^ Butt AN, Swaminathan R (August 2008). "Overview of circulating nucleic acids in plasma/serum". Annals of the New York Academy of Sciences. 1137 (1): 236–42. Bibcode:2008NYASA1137..236B. doi:10.1196/annals.1448.002. PMID 18837954. S2CID 34380267.
  6. ^ Mouliere F, Robert B, Arnau Peyrotte E, Del Rio M, Ychou M, et al. (2011). "High Fragmentation Characterizes Tumour-Derived Circulating DNA". PLOS ONE. 6 (9): e23418. Bibcode:2011PLoSO...623418M. doi:10.1371/journal.pone.0023418. PMC 3167805. PMID 21909401.
  7. ^ Mouliere F, Chandrananda D, Piskorz AM, Moore EK, Morris J, Ahlborn LB, et al. (November 2018). "Enhanced detection of circulating tumor DNA by fragment size analysis". Sci Transl Med. 10 (466). doi:10.1126/scitranslmed.aat4921. PMC 6483061. PMID 30404863.
  8. ^ Gall TM, Belete S, Khanderia E, Frampton AE, Jiao LR (January 2019). "Circulating Tumor Cells and Cell-Free DNA in Pancreatic Ductal Adenocarcinoma". The American Journal of Pathology. 189 (1): 71–81. doi:10.1016/j.ajpath.2018.03.020. hdl:10044/1/58615. PMID 30558725.
  9. ^ Casadio V, Calistri D, Salvi S, Gunelli R, Carretta E, Amadori D, Silvestrini R, Zoli W (2013). "Urine cell-free DNA integrity as a marker for early prostate cancer diagnosis: a pilot study". Biomed Res Int. 2013: 270457. doi:10.1155/2013/270457. PMC 3586456. PMID 23509700.
  10. ^ a b Esfahani, Mohammad Shahrokh; Hamilton, Emily G.; Mehrmohamadi, Mahya; et al. (April 2022). "Inferring gene expression from cell-free DNA fragmentation profiles". Nature Biotechnology. 40 (4): 585–597. doi:10.1038/s41587-022-01222-4. PMC 9337986. PMID 35361996.
  11. ^ Mutter, Jurik A; Shahrokh Esfahani, Mohammad; Schroers-Martin, Joseph; et al. (28 November 2023). "Inferred Gene Expression By Cell-Free DNA Profiling Allows Noninvasive Lymphoma Classification". Blood. 142 (Supplement 1): 245. doi:10.1182/blood-2023-186853.
  12. ^ Alig, Stefan K.; Shahrokh Esfahani, Mohammad; Garofalo, Andrea; et al. (25 January 2024). "Distinct Hodgkin lymphoma subtypes defined by noninvasive genomic profiling". Nature. 625 (7996): 778–787. doi:10.1038/s41586-023-06903-x. PMC 11293530. PMID 38081297.
  13. ^ Teo YV, Capri M, Morsiani C, Pizza G, Faria AM, Franceschi C, Neretti N (February 2019). "Cell-free DNA as a biomarker of aging". Aging Cell. 18 (1): e12890. doi:10.1111/acel.12890. PMC 6351822. PMID 30575273.
  14. ^ Thakur ZH, Becker A, Matei I, Huang Y, Costa-Silva B (2014). "Double-stranded DNA in exosomes: a novel biomarker in cancer detection". Cell Research. 24 (6): 766–9. doi:10.1038/cr.2014.44. PMC 4042169. PMID 24710597.
  15. ^ Roth C, Pantel K, Müller V, Rack B, Kasimir-Bauer S, Janni W, Schwarzenbach H (January 2011). "Apoptosis-related deregulation of proteolytic activities and high serum levels of circulating nucleosomes and DNA in blood correlate with breast cancer progression". BMC Cancer. 11 (1): 4. doi:10.1186/1471-2407-11-4. PMC 3024991. PMID 21211028.
  16. ^ Hudecova I, Smith CG, Hänsel-Hertsch R, Chilamakuri C, Morris JA, Vijayaraghavan A, Heider K, Chandrananda D, Cooper WN, Gale D, Garcia-Corbacho J, Pacey S, Baird R, Rosenfeld N, Mouliere F (2021). "Characteristics, origin, and potential for cancer diagnostics of ultrashort plasma cell-free DNA". Genome Research. 32 (2): 215–227. doi:10.1101/gr.275691.121. PMC 8805718. PMID 34930798.
  17. ^ Stoetzer OJ, Fersching DM, Salat C, Steinkohl O, Gabka CJ, Hamann U, Braun M, Feller AM, Heinemann V, Siegele B, Nagel D, Holdenrieder S (August 2013). "Prediction of response to neoadjuvant chemotherapy in breast cancer patients by circulating apoptotic biomarkers nucleosomes, DNAse, cytokeratin-18 fragments and survivin". Cancer Letters. 336 (1): 140–8. doi:10.1016/j.canlet.2013.04.013. PMID 23612068.