Multidimensional fragmentomic profiling of cell-free DNA released from patient-derived organoids

Lo YMD, Han DSC, Jiang PY, Chiu RWK. Epigenetics, fragmentomics, and topology of cell-free DNA in liquid biopsies. Science. 2021;372:eqqw3616.

Article  Google Scholar 

Chiu RWK, Heitzer E, Lo YMD, Mouliere F, Tsui DWY. Cell-free DNA fragmentomics: the new “omics” on the block. Clin Chem. 2020;66:1480–4.

Article  PubMed  Google Scholar 

Thierry AR. Circulating DNA fragmentomics and cancer screening. Cell Genomics. 2023;3:100242.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bao H, Wang Z, Ma XJ, Guo W, Zhang XY, Tang WXF, Chen X, Wang XY, Chen YK, Mo SB, et al. Letter to the editor: an ultrasensitive assay using cell-free DNA fragmentomics for multicancer early detection. Mol Cancer. 2022;21:1–7.

Article  Google Scholar 

Han DSC, Lo YMD. The nexus of cfDNA and nuclease biology. Trends Genet. 2021;37:758–70.

Article  CAS  PubMed  Google Scholar 

Han DSC, Ni M, Chan RWY, Chan VWH, Lui KO, Chiu RWK, Lo YMD. The biology of cell-free DNA fragmentation and the roles of DNASE1, DNASE1L3, and DFFB. Am J Hum Genet. 2020;106:202–14.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Heitzer E, Auinger L, Speicher MR. Cell-free DNA and apoptosis: how dead cells inform about the living. Trends Mol Med. 2020;26:519–28.

Article  CAS  PubMed  Google Scholar 

Chen M, Zhao H. Next-generation sequencing in liquid biopsy: cancer screening and early detection. Hum Genomics. 2019;13:34.

Article  PubMed  PubMed Central  Google Scholar 

Snyder MW, Kircher M, Hill AJ, Daza RM, Shendure J. Cell-free DNA comprises an in vivo nucleosome footprint that informs its tissues-of-origin. Cell. 2016;164:57–68.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lui YNYN, Chik KW, Chiu RWK, Ho CY, Lam CWK, Lo YMD. Predominant hematopoietic origin of cell-free DNA in plasma and serum after sex-mismatched bone marrow transplantation. Clin Chem. 2002;48:421–7.

Article  CAS  PubMed  Google Scholar 

Moss J, Magenheim J, Neiman D, Zemmour H, Loyfer N, Korach A, Samet Y, Maoz M, Druid H, Arner P, et al. Comprehensive human cell-type methylation atlas reveals origins of circulating cell-free DNA in health and disease. Nat Commun. 2018;9:5068.

Article  PubMed  PubMed Central  Google Scholar 

Stejskal P, Goodarzi H, Srovnal J, Hajdúch M, van’t Veer LJ, Magbanua MJM. Circulating tumor nucleic acids: biology, release mechanisms, and clinical relevance. Mol Cancer. 2023;22:15.

Article  CAS  PubMed  PubMed Central  Google Scholar 

van der Pol Y, Mouliere F. Toward the early detection of cancer by decoding the epigenetic and environmental fingerprints of cell-free DNA. Cancer Cell. 2019;36:350–68.

Article  PubMed  Google Scholar 

Vagner T, Spinelli C, Minciacchi VR, Balaj L, Zandian M, Conley A, Zijlstra A, Freeman MR, Demichelis F, De S, et al. Large extracellular vesicles carry most of the tumor DNA circulating in prostate cancer patient plasma. J Extracell Vesicles. 2018;7:1505403.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ungerer V, Bronkhorst AJ, Van den Ackerveken P, Herzog M, Holdenrieder S. Serial profiling of cell-free DNA and nucleosome histone modifications in cell cultures. Sci Rep. 2021;11:9460.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Panagopoulou M, Karaglani M, Balgkouranidou I, Pantazi C, Kolios G, Kakolyris S, Chatzaki E. Circulating cell-free DNA release in vitro: kinetics, size profiling, and cancer-related gene methylation. J Cell Physiol. 2019;234:14079–89.

Article  CAS  PubMed  Google Scholar 

Bronkhorst AJ, Wentzel JF, Aucamp J, van Dyk E, du Plessis L, Pretorius PJ. Characterization of the cell-free DNA released by cultured cancer cells. BBA-Mol Cell Res. 2016;1863:157–65.

CAS  Google Scholar 

Aucamp J, Calitz C, Bronkhorst AJ, Wrzesinski K, Hamman S, Gouws C, Pretorius PJ. Cell-free DNA in a three-dimensional spheroid cell culture model: a preliminary study. Int J Biochem Cell Biol. 2017;89:182–92.

Article  CAS  PubMed  Google Scholar 

Wang W, Kong P, Ma G, Li L, Zhu J, Xia TS, Xie H, Zhou WB, Wang S. Characterization of the release and biological significance of cell-free DNA from breast cancer cell lines. Oncotarget. 2017;8:43180–91.

Article  PubMed  PubMed Central  Google Scholar 

Kim J, Koo BK, Knoblich JA. Human organoids: model systems for human biology and medicine. Nat Rev Mol Cell Biol. 2020;21:571–84.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Shitara A, Takahashi K, Goto M, Takahashi H, Iwasawa T, Onodera Y, Makino K, Miura H, Shirasawa H, Sato W, et al. Cell-free DNA in spent culture medium effectively reflects the chromosomal status of embryos following culturing beyond implantation compared to trophectoderm biopsy. PLoS ONE. 2021;16:e0246438.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Vera-Rodriguez M, Diez-Juan A, Jimenez-Almazan J, Martinez S, Navarro R, Peinado V, Mercader A, Meseguer M, Blesa D, Moreno I, et al. Origin and composition of cell-free DNA in spent medium from human embryo culture during preimplantation development. Hum Reprod. 2018;33:745–56.

Article  CAS  PubMed  Google Scholar 

Shamonki MI, Jin HL, Haimowitz Z, Liu L. Proof of concept: preimplantation genetic screening without embryo biopsy through analysis of cell-free DNA in spent embryo culture media. Fertil Steril. 2016;106:1312–8.

Article  CAS  PubMed  Google Scholar 

Dantes Z, Yen HY, Pfarr N, Winter C, Steiger K, Muckenhuber A, Hennig A, Lange S, Engleitner T, Ollinger R, et al. Implementing cell-free DNA of pancreatic cancer patient-derived organoids for personalized oncology. Jci Insight. 2020;5:e137809.

Article  PubMed  PubMed Central  Google Scholar 

Heider K, Wan JCM, Hall J, Belic J, Boyle S, Hudecova I, Gale D, Cooper WN, Corrie PG, Brenton JD, et al. Detection of ctDNA from dried blood spots after DNA size selection. Clin Chem. 2020;66:697–705.

Article  PubMed  Google Scholar 

Augustus E, Van Casteren K, Sorber L, van Dam P, Roeyen G, Peeters M, Vorsters A, Wouters A, Raskin J, Rolfo C, et al. The art of obtaining a high yield of cell-free DNA from urine. PLoS ONE. 2020;15:e0231058.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Alcaide M, Cheung M, Hillman J, Rod Rassekh S, Deyell RJ, Batist G, Karsan A, Wyatt AW, Johnson N, Scott DW, et al. Evaluating the quantity, quality and size distribution of cell-free DNA by multiplex droplet digital PCR. Sci Rep. 2020;10:12564.

Article  PubMed  PubMed Central  Google Scholar 

Belmokhtar CA, Hillion J, Segal-Bendirdjian E. Staurosporine induces apoptosis through both caspase-dependent and caspase-independent mechanisms. Oncogene. 2001;20:3354–62.

Article  CAS  PubMed  Google Scholar 

Coleman ML, Sahai EA, Yeo M, Bosch M, Dewar A, Olson MF. Membrane blebbing during apoptosis results from caspase-mediated activation of ROCK I. Nat Cell Biol. 2001;3:339–45.

Article  CAS  PubMed  Google Scholar 

Meddeb R, Pisareva E, Thierry AR. Guidelines for the preanalytical conditions for analyzing circulating cell-free DNA. Clin Chem. 2019;65:623–33.

Article  CAS  PubMed  Google Scholar 

Oreskovic A, Brault ND, Panpradist N, Lai JJ, Lutz BR. Analytical comparison of methods for extraction of short cell-free DNA from urine. J Mol Diagn. 2019;21:1067–78.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Troll CJ, Kapp J, Rao V, Harkins KM, Cole C, Naughton C, Morgan JM, Shapiro B, Green RE. A ligation-based single-stranded library preparation method to analyze cell-free DNA and synthetic oligos. BMC Genomics. 2019;20:1023.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chandrananda D, Thorne NP, Bahlo M. High-resolution characterization of sequence signatures due to nonrandom cleavage of cell-free DNA. BMC Med Genomics. 2015;8:29.

Article  PubMed  PubMed Central  Google Scholar 

Ulz P, Thallinger GG, Auer M, Graf R, Kashofer K, Jahn SW, Abete L, Pristauz G, Petru E, Geigl JB, et al. Inferring expressed genes by whole-genome sequencing of plasma DNA. Nat Genet. 2016;48:1273–8.

Article  CAS  PubMed  Google Scholar 

Ulz P, Perakis S, Zhou Q, Moser T, Belic J, Lazzeri I, Wolfler A, Zebisch A, Gerger A, Pristauz G, et al. Inference of transcription factor binding from cell-free DNA enables tumor subtype prediction and early detection. Nat Commun. 2020;11:4666.

Article  Google Scholar 

Esfahani MS, Hamilton EG, Mehrmohamadi M, Nabe

Comments (0)

No login
gif