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Promoter profiles in plasma CfDNA exhibits a potential utility of predicting the efficacy of neoadjuvant chemotherapy in breast cancer patients.
- Source :
-
Breast cancer research : BCR [Breast Cancer Res] 2024 Jul 04; Vol. 26 (1), pp. 112. Date of Electronic Publication: 2024 Jul 04. - Publication Year :
- 2024
-
Abstract
- Background: Gene expression profiles in breast tissue biopsies contain information related to chemotherapy efficacy. The promoter profiles in cell-free DNA (cfDNA) carrying gene expression information of the original tissues may be used to predict the response to neoadjuvant chemotherapy in breast cancer as a non-invasive biomarker. In this study, the feasibility of the promoter profiles in plasma cfDNA was evaluated as a novel clinical model for noninvasively predicting the efficacy of neoadjuvant chemotherapy in breast cancer.<br />Method: First of all, global chromatin (5 Mb windows), sub-compartments and promoter profiles in plasma cfDNA samples from 94 patients with breast cancer before neoadjuvant chemotherapy (pCR = 31 vs. non-pCR = 63) were analyzed, and then classifiers were developed for predicting the efficacy of neoadjuvant chemotherapy in breast cancer. Further, the promoter profile changes in sequential cfDNA samples from 30 patients (pCR = 8 vs. non-pCR = 22) during neoadjuvant chemotherapy were analyzed to explore the potential benefits of cfDNA promoter profile changes as a novel potential biomarker for predicting the treatment efficacy.<br />Results: The results showed significantly distinct promoter profile in plasma cfDNA of pCR patients compared with non-pCR patients before neoadjuvant chemotherapy. The classifier based on promoter profiles in a Random Forest model produced the largest area under the curve of 0.980 (95% CI: 0.978-0.983). After neoadjuvant chemotherapy, 332 genes with significantly differential promoter profile changes in sequential cfDNA samples of pCR patients was observed, compared with non-pCR patients, and their functions were closely related to treatment response.<br />Conclusion: These results suggest that promoter profiles in plasma cfDNA may be a powerful, non-invasive tool for predicting the efficacy of neoadjuvant chemotherapy breast cancer patients before treatment, and the on-treatment cfDNA promoter profiles have potential benefits for predicting the treatment efficacy.<br /> (© 2024. The Author(s).)
- Subjects :
- Humans
Female
Middle Aged
Adult
Prognosis
Antineoplastic Combined Chemotherapy Protocols therapeutic use
Aged
Treatment Outcome
Gene Expression Profiling
Breast Neoplasms drug therapy
Breast Neoplasms genetics
Breast Neoplasms blood
Breast Neoplasms pathology
Neoadjuvant Therapy
Promoter Regions, Genetic
Biomarkers, Tumor blood
Biomarkers, Tumor genetics
Cell-Free Nucleic Acids blood
Cell-Free Nucleic Acids genetics
Subjects
Details
- Language :
- English
- ISSN :
- 1465-542X
- Volume :
- 26
- Issue :
- 1
- Database :
- MEDLINE
- Journal :
- Breast cancer research : BCR
- Publication Type :
- Academic Journal
- Accession number :
- 38965610
- Full Text :
- https://doi.org/10.1186/s13058-024-01860-3