Biology:Circulating free DNA

From HandWiki
Short description: Degraded DNA fragments circulating in bodily fluids

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]

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.[10]

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.[11]

cfDNA circulates predominantly as nucleosomes, which are nuclear complexes of histones and DNA.[12] cfDNA can also be observed in shorter size ranges (e.g. 50bp) and associated with regulatory elements. [13] 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.[14]

History

Circulating nucleic acids were first discovered by Mandel and Metais in 1948.[15] It was later discovered that the level of cfDNA is significantly increased in the plasma of diseased patients. This discovery was first made in lupus patients[16] and later it was determined that the levels of cfDNA are elevated in over half of cancer patients.[17] Molecular analysis of cfDNA resulted in an important discovery that blood plasma DNA from cancer patients contains tumor-associated mutations and it can be used for cancer diagnostics and follow up.[18][19] The ability to extract circulating tumor DNA (ctDNA) from the human plasma has led to huge advancements in noninvasive cancer detection.[20] Most notably, it has led to what is now known as liquid biopsy. In short, liquid biopsy is using biomarkers and cancer cells in the blood as a means of diagnosing cancer type and stage.[21] This type of biopsy is noninvasive and allows for the routine clinical screening that is important in determining cancer relapse after initial treatment.[22]

Different origins of cfDNA

The intracellular origin of cfDNA, e.g., either from nucleus or mitochondria, can also influence the inflammatory potential of cfDNA. mtDNA is a potent inflammatory trigger.[23] mtDNA, due to its prokaryotic origin, holds many features that are similar to bacterial DNA, including the presence of a relatively high content of unmethylated CpG motifs, which are rarely observed in nuclear DNA.[24] The unmethylated CpG motifs are of particular importance as TLR9, the only endolysosomal DNA-sensing receptor, has a unique specificity for unmethylated CpG DNA. mtDNA was shown to activate neutrophils through TLR9 engagement [25] unless coupled to carrier proteins, mtDNA, but not nuclear DNA, can be recognized as a danger-associated molecular pattern inducing pro-inflammation through TLR9.[26] Collins et al. reported that intra-articular injection of mtDNA induces arthritis in vivo, proposing a direct role of mtDNA extrusion in the disease pathogenesis of RA .[27][26]

MtDNA, in contrast to nuclear DNA, is characterized by elevated basal levels of 8-OHdG, a marker of oxidative damage. The high content of oxidative damage in mtDNA is attributed to the close proximity of mtDNA to ROS and relatively inefficient DNA repair mechanisms that can lead to the accumulation of DNA lesions.[27][28]

They have shown that oxidative burst during NETosis can oxidize mtDNA and the released oxidized mtDNA by itself, or in complex with TFAM, can generate prominent induction of type I IFNs.[23] Oxidized mtDNA generated during programmed cell death is not limited to activate TLR9, but was shown to also engage the NRLP3 inflammasome, leading to the production of pro-inflammatory cytokines, IL-1β, and IL-18.[27][29] MtDNA can also be recognized by cyclic GMP-AMP synthase (cGAS), a cytosolic dsDNA sensor to initiate a STING-IRF3-dependent pathway that in turn orchestrates the production of type I IFNs.[27][30]

Methods

Collection and purification

cfDNA purification is prone to contamination through genomic DNA due to ruptured blood cells during the purification process.[31] Because of this, different purification methods can lead to significantly different cfDNA extraction yields.[32][33] At the moment, typical purification methods involve collection of blood via venipuncture, centrifugation to pellet the cells, and extraction of cfDNA from the plasma. The specific method for extraction of cfDNA from the plasma depends on the protocol desired.[34]

Analysis of cfDNA

PCR

In general, the detection of specific DNA sequences in cfDNA can be done by two means; sequence specific detection (PCR based) and general genomic analysis of all cfDNA present in the blood (DNA sequencing).[35] The presence of cfDNA containing DNA from tumor cells was originally characterized using PCR amplification of mutated genes from extracted cfDNA.[18] PCR based analysis of cfDNA typically rely on the analytical nature of qPCR and digital PCR. Both of these techniques can be sensitive and cost-effective for detecting limited number of hotspots mutations. For this reason the PCR based method of detection is still very prominent tool in cfDNA detection. This method has the limitation of not being able to detect larger structural variant present in ctDNA and for this reason massively parallel next generation sequencing is also used to determine ctDNA content in cfDNA

Massively Parallel Sequencing

Massively parallel sequencing (MPS) has allowed the deep sequencing of cfDNA. This deep sequencing is required to detect mutant ctDNA present in low concentrations in the plasma. Two main sequencing techniques are typically used for targeted analysis of mutant cfDNA; PCR amplicon sequencing[36] and hybrid capture sequencing.[37] Other forms of genetic alterations can be analysed using ctDNA (e.g. somatic copy number alterations or genetic rearrangements). Here, methods based on untargeted sequencing, like WGS or low coverage WGS, are mainly used.

cfDNA and Illness

Cancer

The majority of cfDNA research is focused on DNA originating from cancer (ctDNA). In short, the DNA from cancer cells gets released by cell-death, secretion or other mechanisms still not known.[38] The fraction of cfDNA released by tumor cells in circulation is influenced by the size of the tumor as well as the tumor stage and type. Early stage cancers and brain tumor are among the most difficult to detect with liquid biopsy.[39][40][41]

Trauma

Elevated cfDNA has been detected with acute blunt trauma[42] and burn victims.[43] In both of these cases cfDNA concentration in the plasma were correlated to the severity of the injury, as well as outcome of the patient.

Sepsis

It has been shown that an increase cfDNA in the plasma of ICU patients is an indicator of the onset of sepsis.[44][45] Due to the severity of sepsis in ICU patients, further testing in order to determine the scope of cfDNA efficacy as a biomarker for septic risk is likely.[5]

Myocardial Infarction

Patients showing signs of myocardial infarction have been shown to have elevated cfDNA levels.[46] This elevation correlates to patient outcome in terms of additional cardiac issues and even mortality within two years.[47]

Transplant Graft Rejection

Foreign cfDNA has been shown to be present in the plasma of solid organ transplant patients. This cfDNA is derived from the grafted organ and is termed dd-cfDNA (donor-derived cell-free DNA). Dd-cfDNA values spike initially after a transplant procedure (>5%) with values heavily depending on the transplanted organ and typically drop (<0.5%) within one week for most organs.[48] If the host body rejects the grafted organ the ddcfDNA concentration in the blood (plasma) will rise to a level greater than 5-fold higher than those without complications. This increase in ddcfDNA can be detected prior to any other clinical or biochemical signs of complication.[48] Besides dd-cfDNA in plasma, some research also focused on the excretion of ddcfDNA through urine. This is of special interest in kidney allografts transplantation. When dd-cfDNA is measured using targeted next-generation sequencing, assays were used with a population specific genome wide SNP panel.[49] Attaching barcodes to the ligated adapters prior to NGS during library preparation make absolute ddcfDNA quantification possible without the need for prior donor genotyping.[50] This has been shown to provide additional clinical benefits if the absolute number of cfDNA copies is considered combined together with the fraction of ddcfDNA over cfDNA from the recipient to determine whether the allograft is being rejected or not.[49]

Future directions

ELISA diretto e sandwich.png

cfDNA allows a rapid, easy, non-invasive and repetitive method of sampling. A combination of these biological features and technical feasibility of sampling, position cfDNA as a potential biomarker of enormous utility for example for autoimmune rheumatic diseases and tumors. It offers also a potential biomarker with its own advantages over invasive tissue biopsy as a quantitative measure for detection of transplant rejection as well as immunosuppression optimisation. However, this method lacks uniformity on the type of sample (plasma/serum/synovial fluid/urine), methods of sample collection/processing, free or cell-surface bound DNA, cfDNA extraction and cfDNA quantification, and also in the presentation and interpretation of quantitative cfDNA findings.[27]

cfDNA is quantified by fluorescence methods, such as PicoGreen staining and ultraviolet spectrometry, the more sensitive is quantitative polymerase chain reaction (PCR; SYBR Green or TaqMan) of repetitive elements or housekeeping genes, or deep sequencing methods. Circulating nucleosomes, the primary repeating unit of DNA organization in chromatin, are quantified by enzyme-linked immunosorbent assays (ELISA).[51]

Databases

NucPosDB: a database of nucleosome positioning in vivo and nucleosomics of cell-free DNA

References

  1. ↑ "NucPosDB: a database of nucleosome positioning in vivo and nucleosomics of cell-free DNA". Chromosoma 131 (1–2): 19–28. June 2022. doi:10.1007/s00412-021-00766-9. PMID 35061087. 
  2. ↑ "Adding Insult on Injury: Immunogenic Role for Donor-derived Cell-free DNA?". Transplantation 104 (11): 2266–71. November 2020. doi:10.1097/TP.0000000000003240. PMID 32217943. 
  3. ↑ "Circulating free DNA in the management of breast cancer". Annals of Translational Medicine 2 (1): 3. January 2014. doi:10.3978/j.issn.2305-5839.2013.06.06. PMID 25332979. 
  4. ↑ "The dark side of circulating nucleic acids". Aging Cell 15 (3): 398–9. June 2016. doi:10.1111/acel.12454. PMID 26910468. 
  5. ↑ 5.0 5.1 "Overview of circulating nucleic acids in plasma/serum". Annals of the New York Academy of Sciences 1137 (1): 236–42. August 2008. doi:10.1196/annals.1448.002. PMID 18837954. Bibcode: 2008NYASA1137..236B. 
  6. ↑ "High Fragmentation Characterizes Tumour-Derived Circulating DNA". PLOS ONE 6 (9): e23418. 2011. doi:10.1371/journal.pone.0023418. PMID 21909401. Bibcode: 2011PLoSO...623418M. 
  7. ↑ "Enhanced detection of circulating tumor DNA by fragment size analysis". Sci Transl Med 10 (466). November 2018. doi:10.1126/scitranslmed.aat4921. PMID 30404863. 
  8. ↑ "Circulating Tumor Cells and Cell-Free DNA in Pancreatic Ductal Adenocarcinoma". The American Journal of Pathology 189 (1): 71–81. January 2019. doi:10.1016/j.ajpath.2018.03.020. PMID 30558725. 
  9. ↑ "Urine cell-free DNA integrity as a marker for early prostate cancer diagnosis: a pilot study". Biomed Res Int 2013: 270457. 2013. doi:10.1155/2013/270457. PMID 23509700. 
  10. ↑ "Cell-free DNA as a biomarker of aging". Aging Cell 18 (1): e12890. February 2019. doi:10.1111/acel.12890. PMID 30575273. 
  11. ↑ "Double-stranded DNA in exosomes: a novel biomarker in cancer detection". Cell Research 24 (6): 766–9. 2014. doi:10.1038/cr.2014.44. PMID 24710597. 
  12. ↑ "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. January 2011. doi:10.1186/1471-2407-11-4. PMID 21211028. 
  13. ↑ "Characteristics, origin, and potential for cancer diagnostics of ultrashort plasma cell-free DNA". Genome Research 32 (2): 215–227. 2021. doi:10.1101/gr.275691.121. PMID 34930798. 
  14. ↑ "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. August 2013. doi:10.1016/j.canlet.2013.04.013. PMID 23612068. 
  15. ↑ "Les Acides Nucléiques Du Plasma Sanguin Chez l'Homme". Comptes Rendus des Séances de la Société de Biologie et de ses Filiales 142 (3–4): 241–3. February 1948. PMID 18875018. 
  16. ↑ "Deoxyribonucleic acid (DNA) and antibodies to DNA in the serum of patients with systemic lupus erythematosus". The Journal of Clinical Investigation 45 (11): 1732–40. November 1966. doi:10.1172/jci105479. PMID 4959277. 
  17. ↑ "Free DNA in the serum of cancer patients and the effect of therapy". Cancer Research 37 (3): 646–50. March 1977. PMID 837366. 
  18. ↑ 18.0 18.1 "Point mutations of the N-ras gene in the blood plasma DNA of patients with myelodysplastic syndrome or acute myelogenous leukaemia". British Journal of Haematology 86 (4): 774–779. April 1994. doi:10.1111/j.1365-2141.1994.tb04828.x. PMID 7918071. 
  19. ↑ "K-ras point mutations in the blood plasma DNA of patients with colorectal tumors". Challenges of Modern Medicine: Biotechnology Today 5: 141–150. May 1994. 
  20. ↑ "Soluble normal and mutated DNA sequences from single-copy genes in human blood". Cancer Epidemiology, Biomarkers & Prevention 3 (1): 67–71. January 1994. PMID 8118388. 
  21. ↑ "Update on the types and usage of liquid biopsies in the clinical setting: a systematic review". BMC Cancer 18 (1): 527. May 2018. doi:10.1186/s12885-018-4433-3. PMID 29728089. 
  22. ↑ "Advances in liquid biopsy approaches for early detection and monitoring of cancer". Genome Medicine 10 (1): 21. March 2018. doi:10.1186/s13073-018-0533-6. PMID 29558971. 
  23. ↑ 23.0 23.1 "Neutrophil extracellular traps enriched in oxidized mitochondrial DNA are interferogenic and contribute to lupus-like disease". Nature Medicine 22 (2): 146–53. February 2016. doi:10.1038/nm.4027. PMID 26779811. 
  24. ↑ "Mitochondrial origins". Proc Natl Acad Sci U S A 82 (13): 4443–7. July 1985. doi:10.1073/pnas.82.13.4443. PMID 3892535. Bibcode: 1985PNAS...82.4443Y. 
  25. ↑ "Circulating mitochondrial DAMPs cause inflammatory responses to injury". Nature 464 (7285): 104–7. March 2010. doi:10.1038/nature08780. PMID 20203610. Bibcode: 2010Natur.464..104Z. 
  26. ↑ 26.0 26.1 "Endogenously oxidized mitochondrial DNA induces in vivo and in vitro inflammatory responses". Journal of Leukocyte Biology 75 (6): 995–1000. June 2004. doi:10.1189/jlb.0703328. PMID 14982943. 
  27. ↑ 27.0 27.1 27.2 27.3 27.4 "Cell-Free DNA as a Biomarker in Autoimmune Rheumatic Diseases". Frontiers in Immunology 10: 502. 2019-03-19. doi:10.3389/fimmu.2019.00502. PMID 30941136.  CC-BY icon.svg Material was copied from this source, which is available under a Creative Commons Attribution 4.0 International License.
  28. ↑ "Absence of a Pyrimidine Dimer Repair Mechanism for Mitochondrial DNA in Mouse and Human Cells". Molecular Mechanisms for Repair of DNA. 5B. 1975. 589–91. doi:10.1007/978-1-4684-2898-8_26. ISBN 978-1-4684-2900-8. 
  29. ↑ "Oxidized mitochondrial DNA activates the NLRP3 inflammasome during apoptosis". Immunity 36 (3): 401–14. March 2012. doi:10.1016/j.immuni.2012.01.009. PMID 22342844. 
  30. ↑ "Mitochondrial DNA stress primes the antiviral innate immune response". Nature 520 (7548): 553–7. April 2015. doi:10.1038/nature14156. PMID 25642965. Bibcode: 2015Natur.520..553W. 
  31. ↑ "Predominant hematopoietic origin of cell-free DNA in plasma and serum after sex-mismatched bone marrow transplantation". Clinical Chemistry 48 (3): 421–7. March 2002. doi:10.1093/clinchem/48.3.421. PMID 11861434. 
  32. ↑ "Influence of plasma processing on recovery and analysis of circulating nucleic acids". PLOS ONE 8 (10): e77963. 2013-10-18. doi:10.1371/journal.pone.0077963. PMID 24205045. Bibcode: 2013PLoSO...877963P. 
  33. ↑ "Blood Collection and Cell-Free DNA Isolation Methods Influence the Sensitivity of Liquid Biopsy Analysis for Colorectal Cancer Detection". Pathology & Oncology Research 25 (3): 915–923. January 2018. doi:10.1007/s12253-018-0382-z. PMID 29374860. 
  34. ↑ "Comparison of methods for circulating cell-free DNA isolation using blood from cancer patients: impact on biomarker testing". Translational Lung Cancer Research 5 (6): 665–672. December 2016. doi:10.21037/tlcr.2016.12.03. PMID 28149760. 
  35. ↑ "Cell-free DNA (cfDNA): Clinical Significance and Utility in Cancer Shaped By Emerging Technologies". Molecular Cancer Research 14 (10): 898–908. October 2016. doi:10.1158/1541-7786.MCR-16-0044. PMID 27422709. http://mcr.aacrjournals.org/content/14/10/898. 
  36. ↑ "Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA". Science Translational Medicine 4 (136): 136ra68. May 2012. doi:10.1126/scitranslmed.3003726. PMID 22649089. 
  37. ↑ "An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage". Nature Medicine 20 (5): 548–54. May 2014. doi:10.1038/nm.3519. PMID 24705333. 
  38. ↑ "Cell-free nucleic acids as biomarkers in cancer patients". Nature Reviews. Cancer 11 (6): 426–37. June 2011. doi:10.1038/nrc3066. PMID 21562580. 
  39. ↑ van der Pol Y, Mouliere F (2019). "Toward the early detection of cancer by decoding the epigenetic and environmental fingerprints of cell-free DNA.". Cancer Cell 36 (4): 350–368. doi:10.1016/j.ccell.2019.09.003. PMID 31614115. 
  40. ↑ "Fragmentation patterns and personalized sequencing of cell-free DNA in urine and plasma of glioma patients". EMBO Mol Med 13 (8): e12881. August 2021. doi:10.15252/emmm.202012881. PMID 34291583. 
  41. ↑ "Cell-free DNA as a biomarker in cancer". Extracell Vesicles Circ Nucleic Acid 3 (3): 178–98. August 2022. doi:10.20517/evcna.2022.20. 
  42. ↑ "Plasma DNA as a prognostic marker in trauma patients". Clinical Chemistry 46 (3): 319–23. March 2000. doi:10.1093/clinchem/46.3.319. PMID 10702517. 
  43. ↑ "Plasma cell-free DNA as an indicator of severity of injury in burn patients". Clinical Chemistry and Laboratory Medicine 44 (1): 13–7. 2006. doi:10.1515/CCLM.2006.003. PMID 16375578. 
  44. ↑ "Plasma DNA concentration as a predictor of mortality and sepsis in critically ill patients". Critical Care 10 (2): R60. 2006. doi:10.1186/cc4894. PMID 16613611. 
  45. ↑ "Detection of DNA in the plasma of septic patients". Annals of the New York Academy of Sciences 906 (1): 134–40. April 2000. doi:10.1111/j.1749-6632.2000.tb06603.x. PMID 10818609. Bibcode: 2000NYASA.906..134M. 
  46. ↑ "Elevated cell-free serum DNA detected in patients with myocardial infarction". Clinica Chimica Acta; International Journal of Clinical Chemistry 327 (1–2): 95–101. January 2003. doi:10.1016/S0009-8981(02)00337-6. PMID 12482623. 
  47. ↑ "Plasma beta-globin DNA as a prognostic marker in chest pain patients". Clinica Chimica Acta; International Journal of Clinical Chemistry 368 (1–2): 110–3. June 2006. doi:10.1016/j.cca.2005.12.021. PMID 16480967. 
  48. ↑ 48.0 48.1 "Donor-Derived Cell-Free DNA Is a Novel Universal Biomarker for Allograft Rejection in Solid Organ Transplantation". Transplantation Proceedings 47 (8): 2400–3. October 2015. doi:10.1016/j.transproceed.2015.08.035. PMID 26518940. 
  49. ↑ 49.0 49.1 "Validation of a Clinical-Grade Assay to Measure Donor-Derived Cell-Free DNA in Solid Organ Transplant Recipients". The Journal of Molecular Diagnostics 18 (6): 890–902. November 2016. doi:10.1016/j.jmoldx.2016.07.003. PMID 27727019. 
  50. ↑ "Comparison of methods for donor-derived cell-free DNA quantification in plasma and urine from solid organ transplant recipients". Frontiers in Genetics 14: 1089830. 2023. doi:10.3389/fgene.2023.1089830. PMID 36777723. 
  51. ↑ "Circulating nucleic acids in cancer and pregnancy". Methods 50 (4): 302–7. April 2010. doi:10.1016/j.ymeth.2010.02.004. PMID 20146940. 



Retrieved from "https://handwiki.org/wiki/index.php?title=Biology:Circulating_free_DNA&oldid=3651674"