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

Kathleen Schoofs (UGent) , Maísa Renata Ferro Dos Santos (UGent) , Jilke De Wilde (UGent) , Sofie Roelandt (UGent) , Sofie Van de Velde (UGent) , Philippe Decruyenaere (UGent) , Leander Meuris (UGent) , Olivier Thas (UGent) , Annouck Philippron, Lieven Depypere, et al.
(2024) SCIENTIFIC REPORTS. 14(1).
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Abstract
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.
Keywords
Esophageal adenocarcinoma, cfDNA, Liquid biopsy, DNA methylation, Blood plasma, LIQUID BIOPSY, RECURRENCE

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MLA
Schoofs, Kathleen, et al. “Therapy Response Monitoring in Blood Plasma from Esophageal Adenocarcinoma Patients Using Cell-Free DNA Methylation Profiling.” SCIENTIFIC REPORTS, vol. 14, no. 1, 2024, doi:10.1038/s41598-024-82325-7.
APA
Schoofs, K., Ferro Dos Santos, M. R., De Wilde, J., Roelandt, S., Van de Velde, S., Decruyenaere, P., … De Preter, K. (2024). Therapy response monitoring in blood plasma from esophageal adenocarcinoma patients using cell-free DNA methylation profiling. SCIENTIFIC REPORTS, 14(1). https://doi.org/10.1038/s41598-024-82325-7
Chicago author-date
Schoofs, Kathleen, Maísa Renata Ferro Dos Santos, Jilke De Wilde, Sofie Roelandt, Sofie Van de Velde, Philippe Decruyenaere, Leander Meuris, et al. 2024. “Therapy Response Monitoring in Blood Plasma from Esophageal Adenocarcinoma Patients Using Cell-Free DNA Methylation Profiling.” SCIENTIFIC REPORTS 14 (1). https://doi.org/10.1038/s41598-024-82325-7.
Chicago author-date (all authors)
Schoofs, Kathleen, Maísa Renata Ferro Dos Santos, Jilke De Wilde, Sofie Roelandt, Sofie Van de Velde, Philippe Decruyenaere, Leander Meuris, Olivier Thas, Annouck Philippron, Lieven Depypere, Philippe Nafteux, Hanne Vanommeslaeghe, Elke Van Daele, Piet Pattyn, Jo Vandesompele, and Katleen De Preter. 2024. “Therapy Response Monitoring in Blood Plasma from Esophageal Adenocarcinoma Patients Using Cell-Free DNA Methylation Profiling.” SCIENTIFIC REPORTS 14 (1). doi:10.1038/s41598-024-82325-7.
Vancouver
1.
Schoofs K, Ferro Dos Santos MR, De Wilde J, Roelandt S, Van de Velde S, Decruyenaere P, et al. Therapy response monitoring in blood plasma from esophageal adenocarcinoma patients using cell-free DNA methylation profiling. SCIENTIFIC REPORTS. 2024;14(1).
IEEE
[1]
K. Schoofs et al., “Therapy response monitoring in blood plasma from esophageal adenocarcinoma patients using cell-free DNA methylation profiling,” SCIENTIFIC REPORTS, vol. 14, no. 1, 2024.
@article{01JGXFSR9AXE0K74FSBJ53JDY8,
  abstract     = {{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.}},
  articleno    = {{31112}},
  author       = {{Schoofs, Kathleen and Ferro Dos Santos, Maísa Renata and De Wilde, Jilke and Roelandt, Sofie and Van de Velde, Sofie and Decruyenaere, Philippe and Meuris, Leander and Thas, Olivier and Philippron, Annouck and Depypere, Lieven and Nafteux, Philippe and Vanommeslaeghe, Hanne and Van Daele, Elke and Pattyn, Piet and Vandesompele, Jo and De Preter, Katleen}},
  issn         = {{2045-2322}},
  journal      = {{SCIENTIFIC REPORTS}},
  keywords     = {{Esophageal adenocarcinoma,cfDNA,Liquid biopsy,DNA methylation,Blood plasma,LIQUID BIOPSY,RECURRENCE}},
  language     = {{eng}},
  number       = {{1}},
  pages        = {{11}},
  title        = {{Therapy response monitoring in blood plasma from esophageal adenocarcinoma patients using cell-free DNA methylation profiling}},
  url          = {{http://doi.org/10.1038/s41598-024-82325-7}},
  volume       = {{14}},
  year         = {{2024}},
}
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