Systems epigenetic approach towards non-invasive breast cancer detection
Jazyk angličtina Země Anglie, Velká Británie Médium electronic
Typ dokumentu časopisecké články
Grantová podpora
742432
EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)
634570
EC | EU Framework Programme for Research and Innovation H2020 | H2020 Excellent Science (H2020 Priority Excellent Science)
PubMed
40175335
PubMed Central
PMC11965495
DOI
10.1038/s41467-024-53696-2
PII: 10.1038/s41467-024-53696-2
Knihovny.cz E-zdroje
- MeSH
- dospělí MeSH
- epigeneze genetická * MeSH
- epigenomika * metody MeSH
- lidé středního věku MeSH
- lidé MeSH
- metylace DNA * MeSH
- nádory prsu * genetika diagnóza MeSH
- studie případů a kontrol MeSH
- ústní sliznice metabolismus MeSH
- Check Tag
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
No study has systematically compared the suitability of DNA methylation (DNAme) profiles in non-invasive samples for the detection of breast cancer (BC). We assess non-tumour DNAme in 1,100 cervical, buccal, and blood samples from BC cases and controls and find that cervical samples exhibit the largest nuber of differentially methylated sites, followed by buccal samples. No sites were significant in blood after FDR adjustment. Deriving DNAme-based classifiers for BC detection in each sample type (WID-buccal-, cervical-, or blood-BC), we achieve validation AUCs of 0.75, 0.66, and 0.51, respectively. Buccal and cervical BC-associated DNAme alterations distinguish between BC cases and controls in both surrogate and breast tissue (AUC > 0.88), yet individual sites and the directionality of methylation changes are not identical between these two sample types, and buccal sample DNAme aligns with breast methylation changes more closely. Pending additional validation, these insights may have the potential to improve non-invasive personalized BC prevention.
Centre for Cancer Biomarkers CCBIO Department of Clinical Science University of Bergen Bergen Norway
Department of Medicine and Surgery University of Milano Bicocca Milan Italy
Department of Obstetrics and Gynecology Haukeland University Hospital Bergen Norway
Gynecologic Oncology Program European Institute of Oncology IRCCS Milan Italy
Institute for Biomedical Aging Research Universität Innsbruck Innsbruck Austria
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Sun, Y.-S. et al. Risk factors and preventions of breast cancer. Int. J. Biol. Sci.13, 1387–1397 (2017). PubMed PMC
Clift, A. K. et al. The current status of risk-stratified breast screening. Br. J. Cancer126, 533–550 (2022). PubMed PMC
Pashayan, N. et al. Personalized early detection and prevention of breast cancer: ENVISION consensus statement. Nat. Rev. Clin. Oncol.17, 687–705 (2020). PubMed PMC
Mavaddat, N. et al. Polygenic risk scores for prediction of breast cancer and breast cancer subtypes. Am. J. Hum. Genet.104, 21–34 (2019). PubMed PMC
Moss, J. et al. Circulating breast-derived DNA allows universal detection and monitoring of localized breast cancer. Ann. Oncol.31, 395–403 (2020). PubMed
Cheng, N. et al. Pre-diagnosis plasma cell-free DNA methylome profiling up to seven years prior to clinical detection reveals early signatures of breast cancer. Preprint at 10.1101/2023.01.30.23285027 (2023).
Li, J. et al. Non-invasive biomarkers for early detection of breast cancer. Cancers12, 2767 (2020). PubMed PMC
Barrett, J. E. et al. The WID-BC-index identifies women with primary poor prognostic breast cancer based on DNA methylation in cervical samples. Nat. Commun.13, 449 (2022). PubMed PMC
Adriaanse, M. P. M. et al. Human leukocyte antigen typing using buccal swabs as accurate and non-invasive substitute for venipuncture in children at risk for celiac disease. J. Gastroenterol. Hepatol.31, 1711–1716 (2016). PubMed
Kalil, M. N. A. et al. Performance validation of COVID-19 self-conduct buccal and nasal swabs RTK-antigen diagnostic kit. Diagnostics11, 2245 (2021). PubMed PMC
Herzog, C. et al. DNA methylation at quantitative trait loci (mQTLs) varies with cell type and nonheritable factors and may improve breast cancer risk assessment. Npj Precis. Oncol.7, 1–10 (2023). PubMed PMC
Guo, W., Fensom, G. K., Reeves, G. K. & Key, T. J. Physical activity and breast cancer risk: results from the UK Biobank prospective cohort. Br. J. Cancer122, 726–732 (2020). PubMed PMC
Bryan, A. D., Magnan, R. E., Hooper, A. E. C., Harlaar, N. & Hutchison, K. E. Physical activity and differential methylation of breast cancer genes assayed from saliva: a preliminary investigation. Ann. Behav. Med. Publ. Soc. Behav. Med.45, 89–98 (2013). PubMed PMC
Breeze, C. E. et al. eFORGE v2.0: updated analysis of cell type-specific signal in epigenomic data. Bioinformatics35, 4767–4769 (2019). PubMed PMC
Peters, T. J. et al. Calling differentially methylated regions from whole genome bisulphite sequencing with DMRcate. Nucleic Acids Res.49, e109 (2021). PubMed PMC
Haga, R. B. & Ridley, A. J. Rho GTPases: regulation and roles in cancer cell biology. Small GTPases7, 207–221 (2016). PubMed PMC
Kazmi, N. et al. Rho GTPase gene expression and breast cancer risk: a Mendelian randomization analysis. Sci. Rep.12, 1463 (2022). PubMed PMC
Castagnoli, L., Tagliabue, E. & Pupa, S. M. Inhibition of the Wnt signalling pathway: an avenue to control breast cancer aggressiveness. Int. J. Mol. Sci.21, 9069 (2020). PubMed PMC
Wang, T. et al. A multiplex blood-based assay targeting DNA methylation in PBMCs enables early detection of breast cancer. Nat. Commun.14, 4724 (2023). PubMed PMC
Schrag, D. et al. Blood-based tests for multicancer early detection (PATHFINDER): a prospective cohort study. Lancet402, 1251–1260 (2023). PubMed PMC
Tang, W. et al. Population-specific mutation patterns in breast tumors from African American, European American, and Kenyan patients. Cancer Res. Commun.3, 2244–2255 (2023). PubMed PMC
Zhou, W., Laird, P. W. & Shen, H. Comprehensive characterization, annotation and innovative use of Infinium DNA methylation BeadChip probes. Nucleic Acids Res.45, e22 (2017). PubMed PMC
Barrett, J. E. et al. The DNA methylome of cervical cells can predict the presence of ovarian cancer. Nat. Commun.13, 448 (2022). PubMed PMC
Wu, T. et al. clusterProfiler 4.0: a universal enrichment tool for interpreting omics data. Innovation2, 100141 (2021). PubMed PMC
Herzog, C. M., Theeuwes, B. & Widschwendter, M. Systems epigenetic approach towards non-invasive breast cancer detection: systems. 10.5281/zenodo.13885250 (2024). PubMed PMC