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Background EWS-FLI1 is a chimeric ETS transcription factor that is, due to a chromosomal rearrangement, specifically expressed in Ewing's sarcoma family tumors (ESFT) and is thought to initiate the development of the disease. Previous genomic profiling experiments have identified EWS-FLI1–regulated genes and genes that discriminate ESFT from other sarcomas, but so far a comprehensive analysis of EWS-FLI1–dependent molecular functions characterizing this aggressive cancer is lacking. Methodology/Principal Findings In this study, a molecular function map of ESFT was constructed based on an integrative analysis of gene expression profiling experiments following EWS-FLI1 knockdown in a panel of five ESFT cell lines, and on gene expression data from the same platform of 59 primary ESFT. Out of 80 normal tissues tested, mesenchymal progenitor cells (MPC) were found to fit the hypothesis that EWS-FLI1 is the driving transcriptional force in ESFT best and were therefore used as the reference tissue for the construction of the molecular function map. The interrelations of molecular pathways were visualized by measuring the similarity among annotated gene functions by gene sharing. The molecular function map highlighted distinct clusters of activities for EWS-FLI1 regulated genes in ESFT and revealed a striking difference between EWS-FLI1 up- and down-regulated genes: EWS-FLI1 induced genes mainly belong to cell cycle regulation, proliferation, and response to DNA damage, while repressed genes were associated with differentiation and cell communication. Conclusions/Significance This study revealed that EWS-FLI1 combines by distinct molecular mechanisms two important functions of cellular transformation in one protein, growth promotion and differentiation blockage. By taking MPC as a reference tissue, a significant EWS-FLI1 signature was discovered in ESFT that only partially overlapped with previously published EWS-FLI1–dependent gene expression patterns, identifying a series of novel targets for the chimeric protein in ESFT. Our results may guide target selection for future ESFT specific therapies.

Breast cancer is among the most common malignancies in women. It is well established that progesterone receptor (PR) is a major determinant in the development and progression of breast tumor, as well as in diagnosis and treatment of breast cancer. However, it is still not fully understood how PR affects downstream signaling pathways and cross talks with other intracellular signal transduction pathways. To better define the role played by PR in estrogen receptor (ER)-dependent gene regulation, we have used chromatin immunoprecipitation coupled with next generation sequencing (ChIP-Seq) to examine the in vivo DNA binding by PR. Whole-Genome ChIP-Seq analysis has identified large number of PR binding sites in T-47D breast cancer cells, which are ER-positive and PR-positive. PR binding sites were detected in proximal promoter regions as well as distal regions, with most located in non-proximal regions. The comparison of PR and ER binding sites revealed that a significant of portion of the PR binding sites overlaps with the ER binding sites, indicating a close relationship between PR and ER in ER-dependent gene regulation. The PR motifs were found to be among the most enriched sequence motifs within the PR binding sites. Further analysis using the chromosome conformation capture assay revealed that progesterone induces changes to the chromatin structures of known PR-regulated genes. The ChIP-Seq data, together with the expression profiling and other results, indicate that PR may cooperate with ER and play an important role in ER-dependent gene regulation, mammary epithelial differentiation and breast cancer development. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4612.

Erythrocyte inclusion bodies that are now commonly referred to as Howell-Jolly Bodies (HJB) were originally discovered over 100 years ago by microscopy. These nuclear fragments are observed in the erythrocytes of patients lacking splenic function, but their precise genomic origins are vague. Here we report studies of the genetic content of HJB using a molecular cytogenetic method known as Comparative Genomic Hybridization (CGH). Peripheral blood samples from six splenectomized human donors were studied. All donors had undergone splenectomies prior to this study for diagnostic and therapeutic indications related to underlying neoplastic and autoimmune disease. Ultrasound testing was used to rule out the presence of accessory splenic tissue, and peripheral blood smears confirmed the presence of HJB. Nucleated cells were removed by density gradients and leukocyte filtration for use as patient-matched controls. DNA was isolated from the leukocytes and HJB-containing erythrocytes. The presence of high molecular weight HJB DNA was confirmed in each sample using gel electrophoresis. As expected, it was not possible to obtain sufficient quantities of DNA from the control erythrocytes of healthy individuals with normal splenic function. CGH was performed using equivalent amounts of reference genomic DNA co-hybridized with HJB DNA or matched donor leukocyte DNA. Agilent oligonucleotide CGH arrays were hybridized and scanned according to the manufacturer’s instructions. The control hybridizations (genomic DNA isolated from donor leukocytes) demonstrated standard patterns consistent with the donor’s karyotype. In contrast, the HJB hybridization signals demonstrated an unusual pattern of centromeric-to-telomeric enrichment on each chromatid of each chromosome. The HJB hybridization signals also increased as a function of distance from the centromere according to the chromatid size. The enhanced signal relative to centromeric distance varied considerably between chromosomes, but was remarkably consistent between donors. These data suggest Howell-Jolly Bodies contain a non-random distribution of centromere-depleted chromatin generated after DNA double-strand breakage during erythroid differentiation.