Alu cell-free DNA concentration, Alu index, and LINE-1 hypomethylation as a cancer predictor.
作者： Sung-Joo Hwang , Ji-Won Lee , Jeong-Chan Lee , Min-Koo Park
DOI: 10.1016/J.CLINBIOCHEM.2021.04.021
关键词: DNA methylation 、 Epigenetics 、 Liquid biopsy 、 Cancer research 、 Cancer 、 Alu element 、 Human genome 、 Methylation 、 Real-time polymerase chain reaction 、 Biology
摘要: Abstract Introduction The liquid biopsy approach, a less-invasive diagnostic tool, enables the detection of disease-specific genetic and epigenetic aberrations. Approximately 66–69% human genome may be composed transposable repetitive elements, including Alu LINE-1. This study aimed to investigate whether Alu-derived cell-free DNA (cfDNA) concentrations, index, LINE-1 methylation could used distinguish patients with cancers from healthy individuals. Methods Two sets primers, shorter longer fragments, were amplify followed by quantitation concentration its integrity index. status was then analyzed quantitative PCR using methylation- unmethylation-specific TaqMan probes. Results Both index level significantly different in comparison between lung or breast cancer controls. area under ROC curve hypomethylation 0.742 0.848 for cancer, respectively, 0.724 0.890 respectively. However, fragment correlated hypomethylation. Regression analysis suggested that level, rather than good discriminator cancers. Conclusions investigated genome-wide status; their associations these combinatory panels implemented as triage test discriminate
sci-hub.st 参考文章(26)
Jia Chen, Xinran Xu, Diet, epigenetic, and cancer prevention. Advances in Genetics. ,vol. 71, pp. 237- 255 ,(2010) , 10.1016/B978-0-12-380864-6.00008-0
Krisanee Chalitchagorn, Shanop Shuangshoti, Nusara Hourpai, Narisorn Kongruttanachok, Pisit Tangkijvanich, Duangporn Thong-ngam, Narin Voravud, Virote Sriuranpong, Apiwat Mutirangura, None, Distinctive pattern of LINE-1 methylation level in normal tissues and the association with carcinogenesis Oncogene. ,vol. 23, pp. 8841- 8846 ,(2004) , 10.1038/SJ.ONC.1208137
Namhee Jung, Nam-Yun Cho, Gyeong Hoon Kang, So Yeon Park, An Na Seo, Hae Yoen Jung, Jae Moon Gwak, Alu and LINE-1 Hypomethylation Is Associated with HER2 Enriched Subtype of Breast Cancer PLoS ONE. ,vol. 9, pp. e100429- ,(2014) , 10.1371/JOURNAL.PONE.0100429
Robert Feil, Mario F. Fraga, Epigenetics and the environment: emerging patterns and implications Nature Reviews Genetics. ,vol. 13, pp. 97- 109 ,(2012) , 10.1038/NRG3142
Dharanija Madhavan, Markus Wallwiener, Karin Bents, Manuela Zucknick, Juliane Nees, Sarah Schott, Katarina Cuk, Sabine Riethdorf, Andreas Trumpp, Klaus Pantel, Christof Sohn, Andreas Schneeweiss, Harald Surowy, Barbara Burwinkel, Plasma DNA integrity as a biomarker for primary and metastatic breast cancer and potential marker for early diagnosis Breast Cancer Research and Treatment. ,vol. 146, pp. 163- 174 ,(2014) , 10.1007/S10549-014-2946-2
Martina Barchitta, Annalisa Quattrocchi, Andrea Maugeri, Manlio Vinciguerra, Antonella Agodi, LINE-1 Hypomethylation in Blood and Tissue Samples as an Epigenetic Marker for Cancer Risk: A Systematic Review and Meta-Analysis PLoS ONE. ,vol. 9, pp. e109478- ,(2014) , 10.1371/JOURNAL.PONE.0109478
A. P. Jason de Koning, Wanjun Gu, Todd A. Castoe, Mark A. Batzer, David D. Pollock, Repetitive Elements May Comprise Over Two-Thirds of the Human Genome PLOS Genetics. ,vol. 7, ,(2011) , 10.1371/JOURNAL.PGEN.1002384
Mary E. Norton, Bo Jacobsson, Geeta K. Swamy, Louise C. Laurent, Angela C. Ranzini, Herb Brar, Mark W. Tomlinson, Leonardo Pereira, Jean L. Spitz, Desiree Hollemon, Howard Cuckle, Thomas J. Musci, Ronald J. Wapner, Cell-free DNA Analysis for Noninvasive Examination of Trisomy The New England Journal of Medicine. ,vol. 373, pp. 1589- 1597 ,(2015) , 10.1056/NEJMOA1407349
US DOE Joint Genome Institute: Hawkins Trevor 4 Branscomb Elbert 4 Predki Paul 4 Richardson Paul 4 Wenning Sarah 4 Slezak Tom 4 Doggett Norman 4 Cheng Jan-Fang 4 Olsen Anne 4 Lucas Susan 4 Elkin Christopher 4 Uberbacher Edward 4 Frazier Marvin 4, RIKEN Genomic Sciences Center: Sakaki Yoshiyuki 9 Fujiyama Asao 9 Hattori Masahira 9 Yada Tetsushi 9 Toyoda Atsushi 9 Itoh Takehiko 9 Kawagoe Chiharu 9 Watanabe Hidemi 9 Totoki Yasushi 9 Taylor Todd 9, Genoscope and CNRS UMR-8030: Weissenbach Jean 10 Heilig Roland 10 Saurin William 10 Artiguenave Francois 10 Brottier Philippe 10 Bruls Thomas 10 Pelletier Eric 10 Robert Catherine 10 Wincker Patrick 10, Department of Genome Analysis, Institute of Molecular Biotechnology: Rosenthal André 12 Platzer Matthias 12 Nyakatura Gerald 12 Taudien Stefan 12 Rump Andreas 12, GTC Sequencing Center: Smith Douglas R. 11 Doucette-Stamm Lynn 11 Rubenfield Marc 11 Weinstock Keith 11 Lee Hong Mei 11 Dubois JoAnn 11, Beijing Genomics Institute/Human Genome Center: Yang Huanming 13 Yu Jun 13 Wang Jian 13 Huang Guyang 14 Gu Jun 15, Multimegabase Sequencing Center, The Institute for Systems Biology: Hood Leroy 16 Rowen Lee 16 Madan Anup 16 Qin Shizen 16, Stanford Genome Technology Center: Davis Ronald W. 17 Federspiel Nancy A. 17 Abola A. Pia 17 Proctor Michael J. 17, University of Oklahoma's Advanced Center for Genome Technology: Roe Bruce A. 22 Chen Feng 22 Pan Huaqin 22, Max Planck Institute for Molecular Genetics: Ramser Juliane 23 Lehrach Hans 23 Reinhardt Richard 23, Cold Spring Harbor Laboratory, Lita Annenberg Hazen Genome Center: McCombie W. Richard 24 de la Bastide Melissa 24 Dedhia Neilay 24, GBF—German Research Centre for Biotechnology: Blöcker Helmut 25 Hornischer Klaus 25 Nordsiek Gabriele 25, Scientific management: National Human Genome Research Institute, US National Institutes of Health: Collins Francis fc23a@ nih. gov 46 b Guyer Mark S. 46 Peterson Jane 46 Felsenfeld Adam 46 Wetterstrand Kris A. 46, Stanford Human Genome Center: Myers Richard M. 18 Schmutz Jeremy 18 Dickson Mark 18 Grimwood Jane 18 Cox David R. 18, University of Washington Genome Center: Olson Maynard V. 19 Kaul Rajinder 19 Raymond Christopher 19, Department of Molecular Biology, Keio University School of Medicine: Shimizu Nobuyoshi 20 Kawasaki Kazuhiko 20 Minoshima Shinsei 20, University of Texas Southwestern Medical Center at Dallas: Evans Glen A. 21 49 50 49 Athanasiou Maria 21 Schultz Roger 21, Office of Science, US Department of Energy: Patrinos Aristides 47, Wellcome Trust: Morgan Michael J. 48, None, Initial sequencing and analysis of the human genome. Nature. ,vol. 409, pp. 860- 921 ,(2001) , 10.1038/35057062
C. Bettegowda, M. Sausen, R. J. Leary, I. Kinde, Y. Wang, N. Agrawal, B. R. Bartlett, H. Wang, B. Luber, R. M. Alani, E. S. Antonarakis, N. S. Azad, A. Bardelli, H. Brem, J. L. Cameron, C. C. Lee, L. A. Fecher, G. L. Gallia, P. Gibbs, D. Le, R. L. Giuntoli, M. Goggins, M. D. Hogarty, M. Holdhoff, S.-M. Hong, Y. Jiao, H. H. Juhl, J. J. Kim, G. Siravegna, D. A. Laheru, C. Lauricella, M. Lim, E. J. Lipson, S. K. N. Marie, G. J. Netto, K. S. Oliner, A. Olivi, L. Olsson, G. J. Riggins, A. Sartore-Bianchi, K. Schmidt, l.-M. Shih, S. M. Oba-Shinjo, S. Siena, D. Theodorescu, J. Tie, T. T. Harkins, S. Veronese, T.-L. Wang, J. D. Weingart, C. L. Wolfgang, L. D. Wood, D. Xing, R. H. Hruban, J. Wu, P. J. Allen, C. M. Schmidt, M. A. Choti, V. E. Velculescu, K. W. Kinzler, B. Vogelstein, N. Papadopoulos, L. A. Diaz, Detection of Circulating Tumor DNA in Early- and Late-Stage Human Malignancies Science Translational Medicine. ,vol. 6, pp. 1- 11 ,(2014) , 10.1126/SCITRANSLMED.3007094