The Gene Desert Mammary Carcinoma Susceptibility Locus Mcs1a Regulates Nr2f1 Modifying Mammary Epithelial Cell Differentiation and Proliferation

Abstract

Genome-wide association studies have revealed that many low-penetrance breast cancer susceptibility loci are located in non-protein coding genomic regions; however, few have been characterized. In a comparative genetics approach to model such loci in a rat breast cancer model, we previously identified the mammary carcinoma susceptibility locus Mcs1a. We now localize Mcs1a to a critical interval (277 Kb) within a gene desert. Mcs1a reduces mammary carcinoma multiplicity by 50% and acts in a mammary cell-autonomous manner. We developed a megadeletion mouse model, which lacks 535 Kb of sequence containing the Mcs1a ortholog. Global gene expression analysis by RNA-seq revealed that in the mouse mammary gland, the orphan nuclear receptor gene Nr2f1/Coup-tf1 is regulated by Mcs1a. In resistant Mcs1a congenic rats, as compared with susceptible congenic control rats, we found Nr2f1 transcript levels to be elevated in mammary gland, epithelial cells, and carcinoma samples. Chromatin looping over ∼820 Kb of sequence from the Nr2f1 promoter to a strongly conserved element within the Mcs1a critical interval was identified. This element contains a 14 bp indel polymorphism that affects a human-rat-mouse conserved COUP-TF binding motif and is a functional Mcs1a candidate. In both the rat and mouse models, higher Nr2f1 transcript levels are associated with higher abundance of luminal mammary epithelial cells. In both the mouse mammary gland and a human breast cancer global gene expression data set, we found Nr2f1 transcript levels to be strongly anti-correlated to a gene cluster enriched in cell cycle-related genes. We queried 12 large publicly available human breast cancer gene expression studies and found that the median NR2F1 transcript level is consistently lower in ‘triple-negative’ (ER-PR-HER2-) breast cancers as compared with ‘receptor-positive’ breast cancers. Our data suggest that the non-protein coding locus Mcs1a regulates Nr2f1, which is a candidate modifier of differentiation, proliferation, and mammary cancer risk.

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

“…These data indicate that the two observed TCE chromatin interactions are functionally distinct, and demonstrates a strong positive regulatory relationship between the Mcs5c TCE and Pappa expression, which appears to be dependent on TCE/P4-1 chromatin looping. The Mcs5c TCE/ Pappa P4-1 interaction, therefore, represents another example of a long-distance acting regulatory region, akin to those identified for the Shh [ 28 ] and Sox9 [ 29 ] genes, as well as the previously characterized Mcs1a locus [ 30 ].…”

“…Transcript quantities were calculated as described in Smits et al . [ 30 ], using a standard curve method to calculate C t values and extrapolate quantity values. Sample measurements are an average of 3–4 technical replicates and data were analyzed using SDS software version 2.2.2 (Applied Biosystems).…”

Mechanisms of disseminated cancer cell dormancy: an awakening field

“…Could some of these gains induce DTC dormancy? NR2F1 , a gene that is induced in dormancy models, and that is known to induce quiescence and lineage commitment, is located in the 5q region and was independently found to be linked to a locus that limits progression in breast cancer 134 . Perhaps DTCs overexpressing NR2F1 may remain dormant until additional genetic and/or epigenetic changes override this signal.…”

The role of genetics in estrogen responses: a critical piece of an intricate puzzle

“…In rats, extensive genetic mapping experiments have been conducted to determine the QTLs and individual genes that control the sensitivity of the mammary gland to E 2 . Loci have been identified that regulate mammary cell proliferation and differentiation (29), mammary immune function (30), and susceptibility to E 2 ‐induced mammary cancer (31, 32). Some of these QTLs have been shown to have relevance in humans, making them interesting targets for prediction and prevention of human mammary disease (29, 33).…”