Enhancer transcription reveals subtype-specific gene expression programs controlling breast cancer pathogenesis.

Noncoding transcription is a defining feature of active enhancers, linking transcription factor (TF) binding to the molecular mechanisms controlling gene expression. To determine the relationship between enhancer activity and biological outcomes in breast cancers, we profiled the transcriptomes (using GRO-seq and RNA-seq) and epigenomes (using ChIP-seq) of 11 different human breast cancer cell lines representing five major molecular subtypes of breast cancer, as well as two immortalized ("normal") human breast cell lines. In addition, we developed a robust and unbiased computational pipeline that simultaneously identifies putative subtype-specific enhancers and their cognate TFs by integrating the magnitude of enhancer transcription, TF mRNA expression levels, TF motif P-values, and enrichment of H3K4me1 and H3K27ac. When applied across the 13 different cell lines noted above, the Total Functional Score of Enhancer Elements (TFSEE) identified key breast cancer subtype-specific TFs that act at transcribed enhancers to dictate gene expression patterns determining growth outcomes, including Forkhead TFs, FOSL1, and PLAG1. FOSL1, a Fos family TF, (1) is highly enriched at the enhancers of triple negative breast cancer (TNBC) cells, (2) acts as a key regulator of the proliferation and viability of TNBC cells, but not Luminal A cells, and (3) is associated with a poor prognosis in TNBC breast cancer patients. Taken together, our results validate our enhancer identification pipeline and reveal that enhancers transcribed in breast cancer cells direct critical gene regulatory networks that promote pathogenesis.

Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes.

BACKGROUND: Epigenetic regulators are frequently mutated or aberrantly expressed in a variety of cancers, leading to altered transcription states that result in changes in cell identity, behavior, and response to therapy. RESULTS: To define alterations in epigenetic landscapes in breast cancers, we profiled the distributions of 8 key histone modifications by ChIP-Seq, as well as primary (GRO-seq) and steady state (RNA-Seq) transcriptomes, across 13 distinct cell lines that represent 5 molecular subtypes of breast cancer and immortalized human mammary epithelial cells. DISCUSSION: Using combinatorial patterns of distinct histone modification signals, we defined subtype-specific chromatin signatures to nominate potential biomarkers. This approach identified AFAP1-AS1 as a triple negative breast cancer-specific gene associated with cell proliferation and epithelial-mesenchymal-transition. In addition, our chromatin mapping data in basal TNBC cell lines are consistent with gene expression patterns in TCGA that indicate decreased activity of the androgen receptor pathway but increased activity of the vitamin D biosynthesis pathway. CONCLUSIONS: Together, these datasets provide a comprehensive resource for histone modification profiles that define epigenetic landscapes and reveal key chromatin signatures in breast cancer cell line subtypes with potential to identify novel and actionable targets for treatment.

Advocating for environmental changes to increase access to parks: engaging promotoras and youth leaders.

Access to physical activity opportunities are limited in underserved communities. Community-based programs can increase promotoras and youth leaders' capacity to advocate for built environmental changes. Promotoras and youth leaders were trained on walkability assessment, park audits, and advocacy. The youth and promotoras from one church located adjacent to a park implemented a community survey, conducted walk audits, and engaged in consciousness-raising activities about environmental factors that affect communities. They also mobilized community members to advocate for a nearby park. Advocacy tactics included attending and making presentations at the City Council, planning meetings, organizing health fairs, and speaking to community members. The following changes were made at the park: removed overgrown plants, relocated storage container, increased park security (i.e., lighting, fencing), improved safety (i.e., covered sewer drain, sand lot removed), enhanced amenities (i.e., drinking fountain, bathroom, benches, tables), improved pedestrian safety in park (i.e., leveled the old and added new walking paths), and improved children's play area (i.e., new play equipment, fencing). The current program highlights factors that contributed to park changes and challenges in increasing access to parks. Furthermore, the current study notes steps that other programs can take to make environmental changes.

In pursuit of excellence: the checkpoint journey.

In March 2004, the Wisconsin Hospital Association launched CheckPoints (www.wicheckpoint.org) to provide consumers with information on the quality and safety of hospital care, and to assist hospitals and physicians in quality improvement activities. Since its inception, the state average achievement for all CheckPoint measures has increased or maintained a high initial rate, with 99% of Wisconsin hospitals voluntarily participating. The current state average is greater than 90% or 90 points (scale 0-100 points) on 11 of the original 19 measures. Over the next 2 years, additional measures will be added that will expand the scope of information available on CheckPoint.

Low molecular weight cyclin E is specific in breast cancer and is associated with mechanisms of tumor progression.

Low molecular weight (LMW) isoforms of cyclin E are post-translationally generated in breast cancer cells and are associated with aggressive disease and poor prognosis. In this study, the specificity of LMW cyclin E to cancer cells was determined by measuring cyclin E expression in tumor and non-tumor tissue from 340 breast cancer patients. Our results reveal the LMW isoforms were detected significantly more frequently in breast tumor tissue than in adjacent non-tumor breast tissues (p < 0.0001). The biologic consequences of the LMW isoforms were studied using a non-tumorigenic mammary epithelial cell line transfected with the cyclin E isoforms and resulted in increased clonogenicity, the inability to enter quiescence in response to growth factor deprivation and genomic instability compared to the full-length cyclin E. Biochemical differences between the full-length and the LMW isoforms were also evident. Biacore analyses show that the LMW isoforms have more efficient binding to CDK2 compared to full-length cyclin E, which could account for the unique biologic consequences observed with the expression of LMW cyclin E. The LMW isoforms of cyclin E are tumor specific, and are biochemically and biologically distinct from the full-length cyclin E which could provide a novel role in breast cancer progression.