Therapy response monitoring in blood plasma from esophageal adenocarcinoma patients using cell-free DNA methylation profiling

被引:0
作者
Schoofs, Kathleen [1 ,2 ,3 ]
Ferro Dos Santos, Maisa R. [1 ,3 ]
De Wilde, Jilke [1 ,2 ,4 ]
Roelandt, Sofie [1 ]
van de Velde, Sofie [1 ]
Decruyenaere, Philippe [2 ,5 ]
Meuris, Leander [6 ]
Thas, Olivier [7 ,8 ,9 ]
Philippron, Annouck [3 ,10 ]
Depypere, Lieven [11 ]
Nafteux, Philippe [11 ]
Vanommeslaeghe, Hanne [10 ]
Van Daele, Elke [10 ]
Pattyn, Piet [10 ,12 ]
Vandesompele, Jo [2 ,3 ]
De Preter, Katleen [1 ,3 ]
机构
[1] UGent & CRIG, Ctr Med Biotechnol VIB, Translat Oncogen & Bioinformat Lab, Technol Pk Zwijnaarde 75, B-9052 Ghent, Belgium
[2] Canc Res Inst Ghent CRIG, OncoRNALab, Ghent, Belgium
[3] Univ Ghent, Dept Biomol Med, Corneel Heymanslaan 10, B-9000 Ghent, Belgium
[4] Ghent Univ Hosp, Dept Pathol, Ghent, Belgium
[5] Ghent Univ Hosp, Dept Hematol, Corneel Heymanslaan 10, B-9000 Ghent, Belgium
[6] VIB UGent, Ctr Med Biotechnol, Dept Biochem & Microbiol, Technol Pk Zwijnaarde 75, B-9052 Ghent, Belgium
[7] Hasselt Univ, Data Sci Inst, I BioStat, Agoralaan,Gebouw D, B-3590 Diepenbeek, Belgium
[8] Univ Ghent, Dept Appl Math Comp Sci & Stat, Ghent, Belgium
[9] Univ Wollongong, Natl Inst Appl Stat Res Australia NIASRA, Wollongong, Australia
[10] Ghent Univ Hosp, Dept Gastrointestinal Surg, Corneel Heymanslaan 10, B-9000 Ghent, Belgium
[11] Univ Hosp Leuven, Dept Thorac Surg, Herestr 49, B-3000 Leuven, Belgium
[12] Univ Ghent, Dept Human Struct & Repair, Ghent, Belgium
来源
SCIENTIFIC REPORTS | 2024年 / 14卷 / 01期
关键词
Esophageal adenocarcinoma; cfDNA; Liquid biopsy; DNA methylation; Blood plasma; LIQUID BIOPSY; RECURRENCE;
D O I
10.1038/s41598-024-82325-7
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
Esophageal adenocarcinoma (EAC) is an aggressive cancer characterized by a high risk of relapse post-surgery. Current follow-up methods (serum carcinoembryonic antigen detection and PET-CT) lack sensitivity and reliability, necessitating a novel approach. Analyzing cell-free DNA (cfDNA) from blood plasma emerges as a promising avenue. This study aims to evaluate the cost-effective and genome-wide cell-free reduced representation bisulfite sequencing (cfRRBS) method combined with computational deconvolution for effective disease monitoring in EAC patients. cfDNA methylation profiling with cfRRBS was performed on 162 blood plasma samples from 33 EAC cancer patients and 28 blood plasma samples from 20 healthy donors. The estimated tumor fraction for EAC patients at the time of diagnosis was significantly different from the healthy donor plasma samples (one-sided Wilcoxon rank-sum test: p-value = 0.032). Tumor fractions above 15% and focal gains/amplifications in MYC (chr8), KRAS (chr12), EGFR (chr7) and NOTCH2 (chr1) were observed in four samples of distinct patients at the time metastatic disease was detected. This study showed feasibility to estimate tumor fractions in blood plasma of EAC patients based on cfDNA methylation using cfRRBS and computational deconvolution. Nevertheless, in this study only cancer patients with evidence of metastatic disease show high tumor fractions and copy number alterations.
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页数:11
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