Summary We analyzed primary breast cancers by genomic DNA copy number arrays, DNA methylation, exome sequencing, mRNA arrays, microRNA sequencing and reverse phase protein arrays. Our ability to integrate information across platforms provided key insights into previously-defined gene expression subtypes and demonstrated the existence of four main breast cancer classes when combining data from five platforms, each of which shows significant molecular heterogeneity. Somatic mutations in only three genes (TP53, PIK3CA and GATA3) occurred at > 10% incidence across all breast cancers; however, there were numerous subtype-associated and novel gene mutations including the enrichment of specific mutations in GATA3, PIK3CA and MAP3K1 with the Luminal A subtype. We identified two novel protein expression-defined subgroups, possibly contributed by stromal/microenvironmental elements, and integrated analyses identified specific signaling pathways dominant in each molecular subtype including a HER2/p-HER2/HER1/p-HER1 signature within the HER2-Enriched expression subtype. Comparison of Basal-like breast tumors with high-grade Serous Ovarian tumors showed many molecular commonalities, suggesting a related etiology and similar therapeutic opportunities. The biologic finding of the four main breast cancer subtypes caused by different subsets of genetic and epigenetic abnormalities raises the hypothesis that much of the clinically observable plasticity and heterogeneity occurs within, and not across, these major biologic subtypes of breast cancer.

Summary To characterize somatic alterations in colorectal carcinoma (CRC), we conducted genome-scale analysis of 276 samples, analyzing exome sequence, DNA copy number, promoter methylation, mRNA and microRNA expression. A subset (97) underwent low-depth-of-coverage whole-genome sequencing. 16% of CRC have hypermutation, three quarters of which have the expected high microsatellite instability (MSI), usually with hypermethylation and MLH1 silencing, but one quarter has somatic mismatch repair gene mutations. Excluding hypermutated cancers, colon and rectum cancers have remarkably similar patterns of genomic alteration. Twenty-four genes are significantly mutated. In addition to the expected APC, TP53, SMAD4, PIK3CA and KRAS mutations, we found frequent mutations in ARID1A, SOX9, and FAM123B/WTX. Recurrent copy number alterations include potentially drug-targetable amplifications of ERBB2 and newly discovered amplification of IGF2. Recurrent chromosomal translocations include fusion of NAV2 and WNT pathway member TCF7L1. Integrative analyses suggest new markers for aggressive CRC and important role for MYC-directed transcriptional activation and repression.

Summary Chromatin is composed of DNA and a variety of modified histones and non-histone proteins, which impact cell differentiation, gene regulation and other key cellular processes. We present a genome-wide chromatin landscape for Drosophila melanogaster based on 18 histone modifications, summarized by 9 prevalent combinatorial patterns. Integrative analysis with other data (non-histone chromatin proteins, DNaseI hypersensitivity, GRO-seq reads produced by engaged polymerase, short/long RNA products) reveals discrete characteristics of chromosomes, genes, regulatory elements, and other functional domains. We find that active genes display distinct chromatin signatures that are correlated with disparate gene lengths, exon patterns, regulatory functions, and genomic contexts. We also demonstrate a diversity of signatures among Polycomb targets that include a subset with paused polymerase. This systematic profiling and integrative analysis of chromatin signatures provides insights into how genomic elements are regulated, and will serve as a resource for future experimental investigations of genome structure and function.

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We report that herpes simplex virus type 1 (HSV-1) infection leads to the recruitment of protein kinase C (PKC) to the nuclear rim. In HEp-2 cells, PKC recruitment to the nuclear rim was initiated between 8 h and 12 h postinfection. PKC␦, a proapoptotic kinase, was completely recruited to the nuclear rim upon infection with HSV-1. PKC␣ was less dramatically relocalized mostly at the nuclear rim upon infection, although some PKC␣ remained in the cytoplasm. PKC-specific immunofluorescence was not significantly relocated to the nuclear rim. The U L 34 and U L 31 proteins, as well as their association, were each required for PKC recruitment to the nuclear rim. The HSV-1 U S 3 protein product, a kinase which regulates the phosphorylation state and localization of U L 34, was not required for PKC recruitment to the nuclear rim; however, it was required for proper localization along the nuclear rim, as PKC appeared unevenly distributed along the nuclear rim of cells infected with U S 3 null and kinase-dead mutants. HSV-1 infection induced the phosphorylation of both lamin B and PKC. Elevated lamin B phosphorylation in HSV-1-infected cells was partially reduced by inhibitors of PKC. The data suggest a model in which kinases that normally disassemble the nuclear lamina during apoptosis are recruited to the nuclear membrane through functions requiring U L 31 and U L 34. We hypothesize that the recruitment of PKC functions to phosphorylate lamin B to help modify the nuclear lamina and promote budding of nucleocapsids at the inner nuclear membrane.The nuclear lamina is a filamentous protein meshwork lining the nucleoplasmic face of the inner nuclear membrane (INM) that confers structural support to the nucleus, provides chromatin anchoring sites, and may regulate higher-order chromatin structure and gene expression (14). The lamina is composed primarily of type V intermediate filament proteins called lamins, which have been grouped into two biochemically and functionally distinct categories: A-type and B-type. Like all intermediate filaments, lamins share a tripartite organization consisting of a conserved central ␣-helical rod domain flanked by N-and C-terminal non-␣-helical head and tail domains of variable size and sequence (35). It is understood that individual lamins will dimerize and intertwine via their rod domains and associate in a head-to-tail fashion via the terminal domains, giving rise to rigid filaments that comprise the lamina meshwork.Despite its relative insolubility and structural rigidity, the lamina is a dynamic structure whose disassembly during mitosis is regulated primarily by phosphorylation of the lamins at conserved serine residues flanking the ␣-helical rod domain (15,35). During apoptosis, one step in the irreversible disassembly of the nuclear lamina (26, 36) involves hyperphosphorylation of lamin B proteins by protein kinase C␦ (PKC␦) (4). Distinct from mitotic lamin phosphorylation, major PKC phosphorylation sites on lamin proteins have been mapped to serine residues located in close proximity...

Results of this controlled study indicated that there was significant clinical and histologic improvement in osteoarthritis-affected joints of horses following treatment with ACS, compared with placebo treatment. On the basis of these findings, further controlled clinical trials to assess this treatment are warranted, and investigation of the mechanisms of action of ACS should be pursued concurrently.

mRNA expression profiling has suggested the existence of multiple glioblastoma subclasses, but their number and characteristics vary among studies and the etiology underlying their development is unclear. In this study, we analyzed 261 microRNA expression profiles from the Cancer Genome Atlas (TCGA), identifying five clinically and genetically distinct subclasses of glioblastoma that each related to a different neural precursor cell type. These microRNA-based glioblastoma subclasses displayed microRNA and mRNA expression signatures resembling those of radial glia, oligoneuronal precursors, neuronal precursors, neuroepithelial/neural crest precursors or astrocyte precursors. Each subclass was determined to be genetically distinct, based on the significant differences they displayed in terms of patient race, age, treatment response and survival. We also identified several microRNAs as potent regulators of subclass-specific gene expression networks in glioblastoma. Foremost among these is miR-9, which suppresses mesenchymal differentiation in glioblastoma by downregulating expression of JAK kinases and inhibiting activation of STAT3. Our findings suggest that microRNAs are important determinants of glioblastoma subclasses through their ability to regulate developmental growth and differentiation programs in several transformed neural precursor cell types. Taken together, our results define developmental microRNA expression signatures that both characterize and contribute to the phenotypic diversity of glioblastoma subclasses, thereby providing an expanded framework for understanding the pathogenesis of glioblastoma in a human neurodevelopmental context.

Cells infected with wild-type herpes simplex virus type 1 (HSV-1) show disruption of the organization of the nuclear lamina that underlies the nuclear envelope. This disruption is reflected in changes in the localization and phosphorylation of lamin proteins. Here, we show that HSV-1 infection causes relocalization of the LEM domain protein emerin. In cells infected with wild-type virus, emerin becomes more mobile in the nuclear membrane, and in cells infected with viruses that fail to express UL34 protein (pUL34) and US3 protein (pUS3), emerin no longer colocalizes with lamins, suggesting that infection causes a loss of connection between emerin and the lamina. Infection causes hyperphosphorylation of emerin in a manner dependent upon both pUL34 and pUS3. Some emerin hyperphosphorylation can be inhibited by the protein kinase C␦ (PKC␦) inhibitor rottlerin. Emerin and pUL34 interact physically, as shown by pull-down and coimmunoprecipitation assays. Emerin expression is not, however, necessary for infection, since virus growth is not impaired in cells derived from emerin-null transgenic mice. The results suggest a model in which pUS3 and PKC␦ that has been recruited by pUL34 hyperphosphorylate emerin, leading to disruption of its connections with lamin proteins and contributing to the disruption of the nuclear lamina. Changes in emerin localization, nuclear shape, and lamin organization characteristic of cells infected with wild-type HSV-1 also occur in cells infected with recombinant virus that does not make viral capsids, suggesting that these changes occur independently of capsid envelopment.During primary envelopment, herpes simplex virus type 1 (HSV-1) nucleocapsids translocate from the nucleus to the cytoplasm by budding into the inner nuclear membrane and then fusing with the outer nuclear membrane. The capsid does not, however, have unimpeded access to the inner nuclear membrane. Lining the inside of the inner nuclear membrane is the nuclear lamina, which is composed of a meshwork of proteins with spaces too small for the capsid to move through without some disruption (2,19,65). The lamina meshwork is made up of intermediate filament family proteins called lamins that are linked to the inner nuclear membrane and to intranuclear proteins by association with lamin-associated proteins (LAPs) (reviewed in reference 65). Connection of the network of lamin proteins to the inner nuclear membrane is mediated by integral membrane LAPs, including emerin, lamin B receptor, LAP2-␤, and MAN-1 (26).Emerin is a member of a family of nuclear envelope proteins that share a common sequence called the LEM domain that mediates association with BAF (barrier to autointegration factor) and is important for the assembly of LEM domain proteins into the re-forming nuclear envelope following mitosis (21,37,39). Emerin also contains a lamin-binding domain that helps retain it in the interphase nuclear envelope (6,14,25,37). Emerin is ubiquitously expressed but is not essential for the viability of cells in culture (36). Failure to ...