RESUMEN
Naïve pluripotent stem cells (nPSC) frequently undergo pathological and not readily reversible loss of DNA methylation marks at imprinted gene loci. This abnormality poses a hurdle for using pluripotent cell lines in biomedical applications and underscores the need to identify the causes of imprint instability in these cells. We show that nPSCs from inbred mouse strains exhibit pronounced strain-specific susceptibility to locus-specific deregulation of imprinting marks during reprogramming to pluripotency and upon culture with MAP kinase inhibitors, a common approach to maintain naïve pluripotency. Analysis of genetically highly diverse nPSCs from the Diversity Outbred (DO) stock confirms that genetic variation is a major determinant of epigenome stability in pluripotent cells. We leverage the variable DNA hypomethylation in DO lines to identify several trans-acting quantitative trait loci (QTLs) that determine epigenome stability at either specific target loci or genome-wide. Candidate factors encoded by two multi-target QTLs on chromosomes 4 and 17 suggest specific transcriptional regulators that contribute to DNA methylation maintenance in nPSCs. We propose that genetic variants represent candidate biomarkers to identify pluripotent cell lines with desirable properties and might serve as entry points for the targeted engineering of nPSCs with stable epigenomes. Highlights: Naïve pluripotent stem cells from distinct inbred mouse strains exhibit variable DNA methylation levels at imprinted gene loci.The vulnerability of pluripotent stem cells to loss of genomic imprinting caused by MAP kinase inhibition strongly differs between inbred mouse strains.Genetically diverse pluripotent stem cell lines from Diversity Outbred mouse stock allow the identification of quantitative trait loci controlling DNA methylation stability.Genetic variants may serve as biomarkers to identify naïve pluripotent stem cell lines that are epigenetically stable in specific culture conditions.
RESUMEN
BACKGROUND: Due to increased cancer detection rates (CDR), breast MR (breast MRI) can reduce underdiagnosis of breast cancer compared to conventional imaging techniques, particularly in women with dense breasts. The purpose of this study is to report the additional breast cancer yield by breast MRI in women with dense breasts after receiving a negative screening mammogram. METHODS: For this study we invited consecutive participants of the national German breast cancer Screening program with breast density categories ACR C & D and a negative mammogram to undergo additional screening by breast MRI. Endpoints were CDR and recall rates. This study reports interim results in the first 200 patients. At a power of 80% and considering an alpha error of 5%, this preliminary population size is sufficient to demonstrate a 4/1000 improvement in CDR. RESULTS: In 200 screening participants, 8 women (40/1000, 17.4-77.3/1000) were recalled due to positive breast MRI findings. Image-guided biopsy revealed 5 cancers in 4 patients (one bilateral), comprising four invasive cancers and one case of DCIS. 3 patients revealed 4 invasive cancers presenting with ACR C breast density and one patient non-calcifying DCIS in a woman with ACR D breast density, resulting in a CDR of 20/1000 (95%-CI 5.5-50.4/1000) and a PPV of 50% (95%-CI 15.7-84.3%). CONCLUSION: Our initial results demonstrate that supplemental screening using breast MRI in women with heterogeneously dense and very dense breasts yields an additional cancer detection rate in line with a prior randomized trial on breast MRI screening of women with extremely dense breasts. These findings are highly important as the population investigated constitutes a much higher proportion of women and yielded cancers particularly in women with heterogeneously dense breasts.