Machine learning unveils an immune-related DNA methylation profile in germline DNA from breast cancer patients.
Clin Epigenetics
; 16(1): 66, 2024 May 15.
Article
em En
| MEDLINE
| ID: mdl-38750495
ABSTRACT
BACKGROUND:
There is an unmet need for precise biomarkers for early non-invasive breast cancer detection. Here, we aimed to identify blood-based DNA methylation biomarkers that are associated with breast cancer.METHODS:
DNA methylation profiling was performed for 524 Asian Chinese individuals, comprising 256 breast cancer patients and 268 age-matched healthy controls, using the Infinium MethylationEPIC array. Feature selection was applied to 649,688 CpG sites in the training set. Predictive models were built by training three machine learning models, with performance evaluated on an independent test set. Enrichment analysis to identify transcription factors binding to regions associated with the selected CpG sites and pathway analysis for genes located nearby were conducted.RESULTS:
A methylation profile comprising 51 CpGs was identified that effectively distinguishes breast cancer patients from healthy controls achieving an AUC of 0.823 on an independent test set. Notably, it outperformed all four previously reported breast cancer-associated methylation profiles. Enrichment analysis revealed enrichment of genomic loci associated with the binding of immune modulating AP-1 transcription factors, while pathway analysis of nearby genes showed an overrepresentation of immune-related pathways.CONCLUSION:
This study has identified a breast cancer-associated methylation profile that is immune-related to potential for early cancer detection.Palavras-chave
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Neoplasias da Mama
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Ilhas de CpG
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Metilação de DNA
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Aprendizado de Máquina
Limite:
Adult
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Aged
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Female
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Humans
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Middle aged
Idioma:
En
Revista:
Clin Epigenetics
Ano de publicação:
2024
Tipo de documento:
Article