Prediagnostic breast milk DNA methylation alterations in women who develop breast cancer

Abstract

Prior candidate gene studies have shown tumor suppressor DNA methylation in breast milk related with history of breast biopsy, an established risk factor for breast cancer. To further establish the utility of breast milk as a tissue-specific biospecimen for investigations of breast carcinogenesis, we measured genome-wide DNA methylation in breast milk from women with and without a diagnosis of breast cancer in two independent cohorts. DNA methylation was assessed using Illumina HumanMethylation450k in 87 breast milk samples. Through an epigenome-wide association study we explored CpG sites associated with a breast cancer diagnosis in the prospectively collected milk samples from the breast that would develop cancer compared with women without a diagnosis of breast cancer using linear mixed effects models adjusted for history of breast biopsy, age, RefFreeCellMix cell estimates, time of delivery, array chip and subject as random effect. We identified 58 differentially methylated CpG sites associated with a subsequent breast cancer diagnosis (q-value <0.05). Nearly all CpG sites associated with a breast cancer diagnosis were hypomethylated in cases compared with controls and were enriched for CpG islands. In addition, inferred repeat element methylation was lower in breast milk DNA from cases compared to controls, and cases exhibited increased estimated epigenetic mitotic tick rate as well as DNA methylation age compared with controls. Breast milk has utility as a biospecimen for prospective assessment of disease risk, for understanding the underlying molecular basis of breast cancer risk factors and improving primary and secondary prevention of breast cancer.

Human milk variation is shaped by maternal genetics and impacts the infant gut microbiome

“…In an analysis of single cell RNA-seq across human tissues, LMX1B was most highly expressed in salivary and breast glandular cells 56 . In addition, hypomethylation at a CpG island in LMX1B in human milk samples was associated with subsequent diagnosis of breast cancer in an epigenome-wide association study 57 , suggesting higher expression correlated with breast cancer risk, which is concordant with the direction of effect in our results. We also show that milk eQTLs can be leveraged to understand the effects of milk gene expression on the breastfed infant.…”

Automatic Detection of the Circulating Cell-Free Methylated DNA Pattern of GCM2, ITPRIPL1 and CCDC181 for Detection of Early Breast Cancer and Surgical Treatment Response

“…There is no clinically useful, noninvasive biomarker for early detection of breast cancer. Previous studies reported that the circulating cell-free DNA-based epigenetic assay can detect early breast cancer; however, most previous studies used a smaller plasma sample size [ 16 , 44 , 92 ], did not carry out clinical blood validation [ 46 , 93 ], carried out detection using nipple fluid, which was not easily available in most women [ 40 , 94 ], or used the higher-cost Illumina HumanMethylation450 BeadChip [ 46 , 93 , 95 ], which may be difficult to use as a universal method in the clinic. Evidence has shown that mammography and ultrasonography support the early diagnosis of breast cancer and reduced breast cancer mortality.…”

New Moms Wellness Study: the randomized controlled trial study protocol for an intervention study to increase fruit and vegetable intake and lower breast cancer risk through weekly counseling and supplemental fruit and vegetable box delivery in breastfeeding women

“…We will use the Infinium MethylationEPIC Kit (Illumina) to assess DNA methylation in epithelial cells from bilateral breastmilk samples collected at baseline and 20 weeks as described in a previous study [ 29 ].…”