The Non-coding Mammary Carcinoma Susceptibility Locus, Mcs5c, Regulates Pappa Expression via Age-Specific Chromatin Folding and Allele-Dependent DNA Methylation

Abstract

In understanding the etiology of breast cancer, the contributions of both genetic and environmental risk factors are further complicated by the impact of breast developmental stage. Specifically, the time period ranging from childhood to young adulthood represents a critical developmental window in a woman’s life when she is more susceptible to environmental hazards that may affect future breast cancer risk. Although the effects of environmental exposures during particular developmental Windows of Susceptibility (WOS) are well documented, the genetic mechanisms governing these interactions are largely unknown. Functional characterization of the Mammary Carcinoma Susceptibility 5c, Mcs5c, congenic rat model of breast cancer at various stages of mammary gland development was conducted to gain insight into the interplay between genetic risk factors and WOS. Using quantitative real-time PCR, chromosome conformation capture, and bisulfite pyrosequencing we have found that Mcs5c acts within the mammary gland to regulate expression of the neighboring gene Pappa during a critical mammary developmental time period in the rat, corresponding to the human young adult WOS. Pappa has been shown to positively regulate the IGF signaling pathway, which is required for proper mammary gland/breast development and is of increasing interest in breast cancer pathogenesis. Mcs5c-mediated regulation of Pappa appears to occur through age-dependent and mammary gland-specific chromatin looping, as well as genotype-dependent CpG island shore methylation. This represents, to our knowledge, the first insight into cellular mechanisms underlying the WOS phenomenon and demonstrates the influence developmental stage can have on risk locus functionality. Additionally, this work represents a novel model for further investigation into how environmental factors, together with genetic factors, modulate breast cancer risk in the context of breast developmental stage.

Deciphering the Role of 3D Genome Organization in Breast Cancer Susceptibility

“…In total we identified 538,199 DCIs with counts higher in the WOS (within WOS DCIs) and 534,454 DCIs with counts lower in the WOS compared to outside the WOS (outside WOS DCIs). Among the DCIs, we recapitulated several TCE-Pappa gene interactions that are higher in the WOS compared to outside the WOS (Figure 1C), which is consistent with previous observations that the TCE interacts with Pappa in a WOS-dependent manner (Henning et al, 2016). In parallel, we applied DESeq2 (Love et al, 2014), EBSeq (Leng et al, 2013) and EdgeR (Robinson et al, 2010) to identify differentially expressed (DE) genes between the WOS and outside the WOS (FDR corrected p-val < 0.05, Methods).…”

In silico prediction of high-resolution Hi-C interaction matrices

“…We next investigated the PAPPA gene locus, which is implicated in the development of mammary glands and is of interest in breast cancer studies 31,32 and identified significant interactions in the 1 MB radius around the PAPPA gene using true and predicted counts. The rat ortholog of PAPPA is regulated by a 8.5 kb genomic region called the temporal control element (TCE) in rat mammary epithelial cells 32 . The TCE resides within the MCS5C genomic locus associated with breast cancer susceptibility and is conserved in human and mouse 32 .…”

“…The rat ortholog of PAPPA is regulated by a 8.5 kb genomic region called the temporal control element (TCE) in rat mammary epithelial cells 32 . The TCE resides within the MCS5C genomic locus associated with breast cancer susceptibility and is conserved in human and mouse 32 . When analyzing true counts, we found the largest number of significant interactions in the Hmec cell line (Supplementary Fig.…”

40 YEARS OF IGF1: PAPP-A and cancer

“…Using a rat model, Henning and coworkers reported that the non-coding mammary carcinoma susceptibility locus, Mcs5c, regulates PAPP-A gene expression during a critical time period in mammary development that can affect breast cancer risk (Henning et al 2016). A novel mechanism of PAPP-A regulation during this 'Window of Susceptibility' involves mammary-gland-specific chromatin looping, where a temporal control element within Mcs5c physically interacts with the Pappa locus.…”