163
Views
0
CrossRef citations to date
0
Altmetric
Review

Cell-free DNA as a Plausible Biomarker of Chronic Kidney Disease

ORCID Icon & ORCID Icon
Pages 879-890 | Received 16 Jul 2023, Accepted 20 Sep 2023, Published online: 04 Oct 2023

References

  • GBD 2013 Mortality and Causes of Death Collaborators . Global, regional, and national age-sex specific all-cause and cause-specific mortality for 240 causes of death, 1990-2013: a systematic analysis for the Global Burden of Disease Study 2013. Lancet385(9963), 117–171 (2015).
  • Fletcher BR , DameryS , AiyegbusiOLet al. Symptom burden and health-related quality of life in chronic kidney disease: a global systematic review and meta-analysis. PLOS Med.19(4), e1003954 (2022).
  • George C , MogueoA , OkpechiIet al. Chronic kidney disease in low-income to middle-income countries: the case for increased screening. BMJ Glob. Health2(2), e000256 (2017).
  • Glassock R , WarnockD , DelanayeP. The global burden of chronic kidney disease: estimates, variability and pitfalls. Nat. Rev. Nephrol.13, 104–114 (2017).
  • Jha V , Garcia-GarciaG , IsekiKet al. Chronic kidney disease: global dimension and perspectives. Lancet382, 260–272 (2013).
  • Lozano R , NaghaviM , ForemanKet al. Global and regional mortality from 235 causes of death for 20 age groups in 1990 and 2010: a systematic analysis for the Global Burden of Disease Study 2010. Lancet380(9859), 2095–2128 (2012).
  • Murton M , Goff-LeggettD , BobrowskaAet al. Burden of chronic kidney disease by KDIGO categories of glomerular filtration rate and albuminuria: a systematic review. Adv. Ther.38(1), 180–200 (2021).
  • Xie Y , BoweB , MokdadAHet al. Analysis of the Global Burden of Disease study highlights the global, regional, and national trends of chronic kidney disease epidemiology from 1990 to 2016. Kidney Int.94(3), 567–581 (2018).
  • Thurlow JS , JoshiM , YanGet al. Global epidemiology of end-stage kidney disease and disparities in kidney replacement therapy. Am. J. Nephrol.52(2), 98–107 (2021).
  • Thomas MC , CooperME , ZimmetP. Changing epidemiology of type 2 diabetes mellitus and associated chronic kidney disease. Nat. Rev. Nephrol.12(2), 73–81 (2016).
  • Kalantar-Zadeh K , JafarTH , NitschDet al. Chronic kidney disease. Lancet398(10302), 786–802 (2021).
  • Major RW , ChengMRI , GrantRAet al. Cardiovascular disease risk factors in chronic kidney disease: a systematic review and meta-analysis. PLOS ONE13(3), e0192895 (2018).
  • Műzes G , BohusnéBarta B , SzabóOet al. Cell-Free DNA in the pathogenesis and therapy of non-infectious inflammations and tumors. Biomedicines10(11), 2853 (2022).
  • Drag MH , KilpeläinenTO. Cell-free DNA and RNA-measurement and applications in clinical diagnostics with focus on metabolic disorders. Physiol. Genomics53(1), 33–46 (2021).
  • Heitzer E , AuingerL , SpeicherMR. Cell-free DNA and apoptosis: how dead cells inform about the living. Trends Mol. Med.26(5), 519–528 (2020).
  • Jing Q , LeungCHC , WuAR. Cell-free DNA as biomarker for sepsis by integration of microbial and host information. Clin. Chem.68(9), 1184–1195 (2022).
  • Leffler J , CiacmaK , GullstrandBet al. A subset of patients with systemic lupus erythematosus fails to degrade DNA from multiple clinically relevant sources. Arthritis Res. Ther.17(1), 205 (2015).
  • Duvvuri B , LoodC. Cell-free DNA as a biomarker in autoimmune rheumatic diseases. Front. Immunol.10, 502 (2019).
  • Ulrich BC , PaweletzCP. Cell-free DNA in oncology: gearing up for clinic. Ann. Lab. Med.38(1), 1–8 (2018).
  • Tsuji N , Agbor-EnohS. Cell-free DNA beyond a biomarker for rejection: biological trigger of tissue injury and potential therapeutics. J. Heart Lung Transplant.40(6), 405–413 (2021).
  • Li X , HuR , LuoTet al. Serum cell-free DNA and progression of diabetic kidney disease: a prospective study. BMJ Open Diabetes Res. Care8(1), e001078 (2020).
  • Einbinder Y , ShnaiderA , GhanayemKet al. Elevated circulating cell-free DNA in hemodialysis-treated patients is associated with increased mortality. Am. J. Nephrol.51(11), 852–860 (2020).
  • Lo YMD , HanDSC , JiangPet al. Epigenetics, fragmentomics, and topology of cell-free DNA in liquid biopsies. Science372(6538), eaaw3616 (2021).
  • Meddeb R , DacheZAA , ThezenasSet al. Quantifying circulating cell-free DNA in humans. Sci. Rep.9, 5220 (2019).
  • Bronkhorst AJ , UngererV , DiehlFet al. Towards systematic nomenclature for cell-free DNA. Hum. Genet.140(4), 565–578 (2021).
  • Thierry AR , ElMessaoudi S , GahanPBet al. Origins, structures, and functions of circulating DNA in oncology. Cancer Metastasis Rev.35, 347–376 (2016).
  • Snyder MW , KircherM , HillAJet al. Cell-free DNA comprises an in vivo nucleosome footprint that informs its tissues-of-origin. Cell164, 57–68 (2016).
  • Diaz LA , BardelliA. Liquid biopsies: genotyping circulating tumor DNA. J. Clin. Oncol.32, 579–586 (2014).
  • Kustanovich A , SchwartzR , PeretzTet al. Life and death of circulating cell-free DNA. Cancer Biol. Ther.20(8), 1057–1067 (2019).
  • García Moreira V , dela Cera Martínez T , GagoGonzález Eet al. Increase in and clearance of cell-free plasma DNA in hemodialysis quantified by real-time PCR. Clin. Chem. Lab. Med.44(12), 1410–1415 (2006).
  • Mouliere F , ChandranandaD , PiskorzAMet al. Enhanced detection of circulating tumor DNA by fragment size analysis. Sci. Transl. Med.10(466), eaat4921 (2018).
  • Jahr S , HentzeH , EnglischSet al. DNA fragments in the blood plasma of cancer patients: quantitations and evidence for their origin from apoptotic and necrotic cells. Cancer Res.61(4), 1659–1665 (2001).
  • Beck J , OellerichM , SchulzUet al. Donor-derived cell-free DNA Is a novel universal biomarker for allograft rejection in solid organ transplantation. Transplant. Proc.47(8), 2400–2403 (2015).
  • Bianchi DW , ChiuRWK. Sequencing of circulating cell-free DNA during pregnancy. N. Engl. J. Med.379(5), 464–473 (2018).
  • Arosemena M , MeahFA , MatherKJet al. Cell-free DNA fragments as biomarkers of islet β-cell death in obesity and type 2 diabetes. Int. J. Mol. Sci.22(4), 2151 (2021).
  • Syed F , TerseySA , TuratsinzeJVet al. Circulating unmethylated CHTOP and INS DNA fragments provide evidence of possible islet cell death in youth with obesity and diabetes. Clin. Epigenetics12(1), 116 (2020).
  • Liu Y , TanQ , LiuF. Differentially methylated circulating DNA: a novel biomarker to monitor beta cell death. J. Diabetes Complications32(3), 349–353 (2018).
  • Jaramillo-Morales J , KorucuB , PikeMMet al. Effects of caloric restriction and aerobic exercise on circulating cell-free mitochondrial DNA in patients with moderate to severe chronic kidney disease. Am. J. Physiol. Renal Physiol.322(1), F68–F75 (2022).
  • Park SS , JeongH , AndreazzaAC. Circulating cell-free mitochondrial DNA in brain health and disease: a systematic review and meta-analysis. World J. Biol. Psychiatry23(2), 87–102 (2022).
  • Zawrotniak M , Rapala-KozikM. Neutrophil extracellular traps (NETs) – formation and implications. Acta Biochim. Pol.60(3), 277–284 (2013).
  • Frangou E , VassilopoulosD , BoletisJet al. An emerging role of neutrophils and NETosis in chronic inflammation and fibrosis in systemic lupus erythematosus (SLE) and ANCA-associated vasculitides (AAV): implications for the pathogenesis and treatment. Autoimmun. Rev.18(8), 751–760 (2019).
  • Brodbeck K , SchickS , BayerBet al. Biological variability of cell-free DNA in healthy females at rest within a short time course. Int. J. Legal. Med.134(3), 911–919 (2020).
  • Alborelli I , GeneraliD , JermannPet al. Cell-free DNA analysis in healthy individuals by next-generation sequencing: a proof of concept and technical validation study. Cell Death Dis.10(7), 534 (2019).
  • Haller N , TomaskovicA , StögglTet al. Feasibility of cell-free DNA measurement from the earlobe during physiological exercise testing. Diagnostics (Basel)12(6), 1379 (2022).
  • Walczak K , StawskiR , PerdasEet al. Circulating cell free DNA response to exhaustive exercise in average trained men with type I diabetes mellitus. Sci. Rep.11(1), 4639 (2021).
  • Nie S , LuJ , WangL , GaoM. Pro-inflammatory role of cell-free mitochondrial DNA in cardiovascular diseases. IUBMB Life72(9), 1879–1890 (2020).
  • Berezina TA , KopytsyaMP , PetyuninaOVet al. Lower circulating cell-free mitochondrial DNA is associated with heart failure in type 2 diabetes mellitus patients. Cardiogenetics13(1), 15–30 (2023).
  • Zhang Q , HeX , LingJet al. Association between circulating cell-free DNA level at admission and the risk of heart failure incidence in acute myocardial infarction patients. DNA Cell Biol.41(8), 742–749 (2022).
  • Dias S , WillmerT , AdamS , PheifferC. The role of maternal DNA methylation in pregnancies complicated by gestational diabetes. Front. Clin. Diabetes Healthc.3, 982665 (2022).
  • Del Vecchio G , LiQ , LiWet al. Cell-free DNA methylation and transcriptomic signature prediction of pregnancies with adverse outcomes. Epigenetics16(6), 642–661 (2021).
  • Hopkins MK , KoelperN , BenderWet al. Association between cell-free DNA fetal fraction and gestational diabetes. Prenat. Diagn.40(6), 724–727 (2020).
  • Linares-Pineda TM , Gutiérrez-RepisoC , Peña-MonteroNet al. Higher β cell death in pregnant women, measured by DNA methylation patterns of cell-free DNA, compared to new-onset type 1 and type 2 diabetes subjects: a cross-sectional study. Diabetol. Metab. Syndr.15(1), 115 (2023).
  • Lappas M , GeorgiouHM , WillcoxJCet al. Postpartum circulating cell-free insulin DNA levels are higher in women with previous gestational diabetes mellitus who develop type 2 diabetes in later life. J. Diabetes Res.2019, 3264184 (2019).
  • El Tarhouny SA , HadhoudKM , EbrahemMMet al. Assessment of cell-free DNA with microvascular complication of type II diabetes mellitus, using PCR and ELISA. Nucleosides Nucleotides Nucleic Acids29, 228–236 (2010).
  • Hu J , WangY , XiangXet al. Serum bisphenol A as a predictor of chronic kidney disease progression in primary hypertension: a 6-year prospective study. J. Hypertens.34, 332–337 (2016).
  • Chang CC , ChiuPF , WuCLet al. Urinary cell-free mitochondrial and nuclear deoxyribonucleic acid correlates with the prognosis of chronic kidney diseases. BMC Nephrol.20(1), 391 (2019).
  • McGuire AL , UrosevicN , ChanDTet al. The impact of chronic kidney disease and short-term treatment with rosiglitazone on plasma cell-free DNA levels. PPAR Res.2014, 643189 (2014).
  • Zhang Y , ZhaoY , WenSet al. Associations of mitochondrial haplogroups and mitochondrial DNA copy numbers with end-stage renal disease in a Han population. Mitochondrial DNA A: DNA Mapp. Seq. Anal.28(5), 725–731 (2017).
  • Ozkaya O , BekK , BedirAet al. Plasma cell-free DNA levels in children on peritoneal dialysis. Nephron Clin. Pract.113(4), c258–c261 (2009).
  • Korabecna M , OpatrnaS , WirthJet al. Cell-free plasma DNA during peritoneal dialysis and hemodialysis and in patients with chronic kidney disease. Ann. NY Acad. Sci.1137, 296–301 (2008).
  • Opatrna S , WirthJ , KorabecnaM , SefrnaF. Cell-free plasma DNA during hemodialysis. Ren. Fail.31(6), 475–480 (2009).
  • Cichota LC , BochiGV , TatschEet al. Circulating double-stranded DNA in plasma of hemodialysis patients and its association with iron stores. Clin. Lab.61(8), 985–990 (2015).
  • Tovbin D , NovackV , WiessmanMPet al. Circulating cell-free DNA in hemodialysis patients predicts mortality. Nephrol. Dial. Transplant.27(10), 3929–3935 (2012).
  • Atamaniuk J , KopeckyC , SkoupySet al. Apoptotic cell-free DNA promotes inflammation in haemodialysis patients. Nephrol. Dial. Transplant.27(3), 902–905 (2012).
  • Kim K , JungSW , ChoWHet al. Associations between cell-free mitochondrial DNA and inflammation, and their clinical implications for patients on hemodialysis: a prospective multicenter cohort study. Blood Purif.50(2), 214–221 (2021).
  • Fan Z , GuoY , ZhongXY. Circulating Cell-free mitochondrial DNA: a potential blood-based biomarker for sarcopenia in patients undergoing maintenance hemodialysis. Med. Sci. Monit.28, e934679 (2022).
  • Jeong JC , KimJE , GuJYet al. Significance of the DNA–histone complex level as a predictor of major adverse cardiovascular events in hemodialysis patients: the effect of uremic toxin on DNA–histone complex formation. Blood Purif.41(1–3), 64–71 (2016).
  • Gaál Kovalčíková A , Janovičovἠ, HodosyJet al. Extracellular DNA concentrations in various aetiologies of acute kidney injury. Sci. Rep.12(1), 16812 (2022).
  • Gisterå A , HanssonGK. The immunology of atherosclerosis. Nat. Rev. Nephrol.13(6), 368–380 (2017).
  • Goligorsky MS . NET formation in dialysis: a valuable, albeit mysterious and enticing predictor of mortality. Am. J. Nephrol.51(11), 849–851 (2020).
  • Kant S , BrennanDC. Donor derived cell free DNA in kidney transplantation: the circa 2020–2021 update. Transpl. Int.35, 10448 (2022).
  • Oellerich M , SherwoodK , KeownPet al. Liquid biopsies: donor-derived cell-free DNA for the detection of kidney allograft injury. Nat. Rev. Nephrol.17(9), 591–603 (2021).
  • Oellerich M , BuddeK , OsmanodjaBet al. Donor-derived cell-free DNA for personalized immunosuppression in renal transplantation. Ther. Drug Monit.45(1), 20–25 (2023).
  • Khush KK , PatelJ , PinneySet al. Noninvasive detection of graft injury after heart transplant using donor-derived cell-free DNA: a prospective multicenter study. Am. J. Transplant.19(10), 2889–2899 (2019).
  • Zhang H , ZhengC , LiXet al. Diagnostic performance of donor-derived plasma cell-free DNA fraction for antibody-mediated rejection in post renal transplant recipients: a prospective observational study. Front. Immunol.11, 342 (2020).
  • Bloom RD , BrombergJS , PoggioEDet al.; Circulating Donor-Derived Cell-Free DNA in Blood for Diagnosing Active Rejection in Kidney Transplant Recipients (DART) Study Investigators. Cell-free DNA and active rejection in kidney allografts. J. Am. Soc. Nephrol.28(7), 2221–2232 (2017).
  • Oellerich M , ShipkovaM , AsendorfTet al. Absolute quantification of donor-derived cell-free DNA as a marker of rejection and graft injury in kidney transplantation: results from a prospective observational study. Am. J. Transplant.19(11), 3087–3099 (2019).
  • Mayer KA , DobererK , TillgrenAet al. Diagnostic value of donor-derived cell-free DNA to predict antibody-mediated rejection in donor-specific antibody-positive renal allograft recipients. Transpl. Int.34(9), 1689–1702 (2021).
  • Halloran PF , ReeveJ , Madill-ThomsenKSet al.; Trifecta Investigators. The Trifecta study: comparing plasma levels of donor-derived cell-free DNA with the molecular phenotype of kidney transplant biopsies. J. Am. Soc. Nephrol.33(2), 387–400 (2022).
  • Obrișcă B , ButiuM , SibuleskyLet al. Combining donor-derived cell-free DNA and donor specific antibody testing as non-invasive biomarkers for rejection in kidney transplantation. Sci. Rep.12(1), 15061 (2022).
  • Jordan SC , BunnapradistS , BrombergJSet al. Donor-derived cell-free DNA identifies antibody-mediated rejection in donor specific antibody positive kidney transplant recipients. Transplant. Direct.4(9), e379 (2018).
  • Butiu M , ObriscaB , SibuleskyLet al. Donor-derived cell-free DNA complements de novo class ii DSA in detecting late alloimmune injury post kidney transplantation. Transplant. Direct.8(2), e1285 (2022).
  • Wolf-Doty TK , MannonRB , PoggioEDet al. Dynamic response of donor-derived cell-free DNA following treatment of acute rejection in kidney allografts. Kidney3602(4), 729–736 (2021).
  • Gielis EM , LedeganckKJ , DeWinter BYet al. Cell-free DNa: an upcoming biomarker in transplantation. Am. J. Transplant.15(10), 2541–2551 (2015).
  • Shen J , ZhouY , ChenYet al. Dynamics of early post-operative plasma ddcf-DNA levels in kidney transplantation: a single-center pilot study. Transpl. Int.32(2), 184–192 (2019).
  • Osmanodja B , AkifovaA , OellerichMet al. Donor-derived cell-free DNA for kidney allograft surveillance after conversion to belatacept: prospective pilot study. J. Clin. Med.12(6), 2437 (2023).
  • Gielis EM , LedeganckKJ , DendoovenAet al. The use of plasma donor-derived, cell-free DNA to monitor acute rejection after kidney transplantation. Nephrol. Dial. Transplant.35(4), 714–721 (2020).
  • Huang E , MengelM , Clahsen-vanGroningen MC , JacksonAM. Diagnostic potential of minimally invasive biomarkers: a biopsy-centered viewpoint from the Banff Minimally Invasive Diagnostics Working Group. Transplantation107(1), 45–52 (2023).

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.