Epigenetic changes with age primes mammary luminal epithelia for cancer initiation

Abstract

Aging causes molecular changes that manifest as stereotypical phenotypes yet aging-associated diseases progress only in certain individuals. At lineage-specific resolution, we show how stereotyped and variant responses are integrated in mammary epithelia. Age-dependent directional changes in gene expression and DNA methylation (DNAm) occurred almost exclusively in luminal cells and implicated genome organizers SATB1 and CTCF. DNAm changes were robust indicators of aging luminal cells, and were either directly (anti-)correlated with expression changes or served as priming events for subsequent dysregulation, such as demethylation of ESR1-binding regions in DNAm-regulatory CXXC5 in older luminal cells and luminal-subtype cancers. Variance-driven changes in the transcriptome of both luminal and myoepithelial lineages further contributed to age-dependent loss of lineage fidelity. The pathways affected by transcriptomic and DNAm changes during aging are commonly linked with breast cancer, and together with the differential variability found across individuals, influence aging-associated cancer susceptibility in a subtype-specific manner.

Breast-Specific Molecular Clocks Comprised ofELF5Expression and Promoter Methylation Identify Individuals Susceptible to Cancer Initiation

“…RNA-sequencing pre-processing is fully described in (14) ) was calculated and a linear regression between organoid and HMEC mean expression was plotted in (Figure 1). During quality control assessment, genes with low counts were determined using edgeR's filterbyExpr function with experimental design group and batch as covariates in the design matrix and were removed.…”

“…Lineage-specific (young <30y LEp vs. <30y MEp) and age-dependent (young <30y LEp vs. >55y LEp) differential expression analysis in the subset of 4 th passage Reduction mammoplasty LEps and MEps was conducted using limma's voom function as described (14) blocking, and design group and batch were modeled in the design matrix. Moderated statistics were computed using eBayes function in limma.…”

“…P-values were adjusted for multiple-testing using Benjamini-Hochberg method. ELF5 differential expression in <30y and >55y in 4th passage LEps and MEps were obtained from (14). Statistical comparison of lineage-specific (young <30y LEp vs. <30y MEp) and age-dependent (young <30y LEp vs. >55y LEp) ELF5 expression in Reduction mammoplasty organoids was performed using a two-sided Welch t-test.…”

“…Cancer Research. Illumina 450K array IDAT files pre-processing is fully described (14). Briefly, IDAT values were loaded and detection p-value filtering was conducted across the dataset in ChAMP package.…”

“…Age-dependent DNA methylation changes were reported in whole breast tissue at gene regulatory elements, at sites that show further alteration in cancer tissues (11,12). We previously showed that DNA methylation and gene expression patterns in luminal epithelial cells shifted toward that of the myoepithelial lineage in an age-dependent manner (13,14). The luminal-specific transcription factor ELF5, E74-like factor 5, stood out as a potential breast-specific aging biomarker because it exhibited excellent dynamic range of gene expression between luminal epithelial cells collected from average-risk younger (<30y) and older (>55y) women (13).…”