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

Autor: Schoofs K; Translational Oncogenomics and Bioinformatics Lab, Center for Medical Biotechnology, VIB-UGent & CRIG, Technologiepark-Zwijnaarde 75, 9052, Ghent, Belgium.; OncoRNALab, Cancer Research Institute Ghent (CRIG), Ghent, Belgium.; Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium., Ferro Dos Santos MR; Translational Oncogenomics and Bioinformatics Lab, Center for Medical Biotechnology, VIB-UGent & CRIG, Technologiepark-Zwijnaarde 75, 9052, Ghent, Belgium.; Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium., De Wilde J; Translational Oncogenomics and Bioinformatics Lab, Center for Medical Biotechnology, VIB-UGent & CRIG, Technologiepark-Zwijnaarde 75, 9052, Ghent, Belgium.; OncoRNALab, Cancer Research Institute Ghent (CRIG), Ghent, Belgium.; Department of Pathology, Ghent University Hospital, Ghent, Belgium., Roelandt S; Translational Oncogenomics and Bioinformatics Lab, Center for Medical Biotechnology, VIB-UGent & CRIG, Technologiepark-Zwijnaarde 75, 9052, Ghent, Belgium., Van de Velde S; Translational Oncogenomics and Bioinformatics Lab, Center for Medical Biotechnology, VIB-UGent & CRIG, Technologiepark-Zwijnaarde 75, 9052, Ghent, Belgium., Decruyenaere P; OncoRNALab, Cancer Research Institute Ghent (CRIG), Ghent, Belgium.; Department of Hematology, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium., Meuris L; Department of Biochemistry and Microbiology, Center for Medical Biotechnology, VIB-UGent, Technologiepark-Zwijnaarde 75, 9052, Ghent, Belgium., Thas O; I-BioStat, Data Science Institute, Hasselt University, Agoralaan Gebouw D, 3590, Diepenbeek, Belgium.; Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium.; National Institute for Applied Statistics Research Australia (NIASRA), University of Wollongong, Wollongong, Australia., Philippron A; Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium.; Department of Gastro-Intestinal Surgery, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium., Depypere L; Department of Thoracic Surgery, University Hospital Leuven, Herestraat 49, 3000, Leuven, Belgium., Nafteux P; Department of Thoracic Surgery, University Hospital Leuven, Herestraat 49, 3000, Leuven, Belgium., Vanommeslaeghe H; Department of Gastro-Intestinal Surgery, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium., Van Daele E; Department of Gastro-Intestinal Surgery, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium., Pattyn P; Department of Gastro-Intestinal Surgery, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium.; Department of Human Structure and Repair, Ghent University, Ghent, Belgium., Vandesompele J; OncoRNALab, Cancer Research Institute Ghent (CRIG), Ghent, Belgium.; Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium., De Preter K; Translational Oncogenomics and Bioinformatics Lab, Center for Medical Biotechnology, VIB-UGent & CRIG, Technologiepark-Zwijnaarde 75, 9052, Ghent, Belgium. Katleen.DePreter@UGent.be.; Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium. Katleen.DePreter@UGent.be.
Jazyk: angličtina
Zdroj: Scientific reports [Sci Rep] 2024 Dec 28; Vol. 14 (1), pp. 31112. Date of Electronic Publication: 2024 Dec 28.
DOI: 10.1038/s41598-024-82325-7
Abstrakt: 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.
Competing Interests: Declarations. Competing interests: The authors declare no competing interests. Ethics: Written informed consent was obtained from all cancer patients and healthy donors. Sample collection was approved by the ethics committee of Ghent University Hospital (registration numbers B670201628317, B670201628319 and B670201733701). The research was conducted according to the local legislation and institutional requirements.
(© 2024. The Author(s).)
Databáze: MEDLINE
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