AbstractBackgroundRisk prediction is crucial for early detection and prognosis of breast cancer. Circulating plasma proteins could provide a valuable source to increase the validity of risk prediction models, however, no such markers have yet been identified for clinical use.MethodsEDTA plasma samples from 183 breast cancer cases and 366 age-matched controls were collected prior to diagnosis from the Swedish breast cancer cohort KARMA. The samples were profiled on 700 circulating proteins using an exploratory affinity proteomics approach. Linear association analyses were performed on case-control status and a data-driven analysis strategy was applied to cluster the women on their plasma proteome profiles in an unsupervised manner. The resulting clusters were subsequently annotated for the differences in phenotypic characteristics, clinical parameters, and genetic risk.ResultsUsing the data-driven approach we identified five clusters with distinct proteomic plasma profiles. Women in a particular sub-group (cluster 1) were significantly more likely to have used menopausal hormonal therapy (MHT), more likely to get a breast cancer diagnosis, and were older compared to the remaining clusters. The levels of circulating proteins in cluster 1 were decreased for proteins related to DNA repair and cell replication and increased for proteins related to mammographic density and female tissues. In contrast, classical dichotomous case-control analyses did not reveal any proteins significantly associated with future breast cancer.ConclusionUsing a data-driven approach, we identified a subset of women with circulating proteins associated with previous use of MHT and risk of breast cancer. Our findings point to the potential long-lasting effects of MHT on the circulating proteome even after ending the treatment, and hence provide valuable insights concerning risk predication of breast cancer.HighlightsCurrent risk prediction models use a variety of factors to identify women at risk of developing breast cancer.Proteins circulating in blood represent an attractive but currently still underrepresented source of candidates serving as molecular risk factors.Plasma proteomes from women participating in a prospective breast cancer cohort study were studied for proteomic risk factors related to a future breast cancer diagnosis.Using data-driven approaches, women with future breast cancers and previous use of menopausal hormone therapy were identified based on their circulating proteins.Menopausal hormone therapy was found to altered the levels of the circulating proteins even years after the treatment ended.