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In cancer, oncogene activation is partly mediated by acquired superenhancers, which therefore represent potential targets for inhibition. Superenhancers are enriched for BRD4 and Mediator, and both BRD4 and the Mediator MED12 subunit are disproportionally required for expression of superenhancer-associated genes in stem cells. Here we show that depletion of Mediator kinase module subunit MED12 or MED13 together with MED13L can be used to reduce expression of cancer-acquired superenhancer genes, such as the MYC gene, in colon cancer cells, with a concomitant decrease in proliferation. Whereas depletion of MED12 or MED13/MED13L caused a disproportional decrease of superenhancer gene expression, this was not seen with depletion of the kinases cyclin-dependent kinase 9 (CDK8) and CDK19. MED12-MED13/MED13L-dependent superenhancer genes were coregulated by beta-catenin, which has previously been shown to associate with MED12. Importantly, beta-catenin depletion caused reduced binding of MED12 at the MYC superenhancer. The effect of MED12 or MED13/MED13L depletion on cancer-acquired superenhancer gene expression was more specific than and partially distinct from that of BRD4 depletion, with the most efficient inhibition seen with combined targeting. These results identify a requirement of MED12 and MED13/MED13L for expression of acquired superenhancer genes in colon cancer, implicating these Mediator subunits as potential therapeutic targets for colon cancer, alone or together with BRD4.

1700692 Fully addressable DNA nanostructures, especially DNA origami, possess huge potential to serve as inherently biocompatible and versatile molecular platforms. However, their use as delivery vehicles in therapeutics is compromised by their low stability and poor transfection rates. This study shows that DNA origami can be coated by precisely defined one-to-one protein-dendron conjugates to tackle the aforementioned issues. The dendron part of the conjugate serves as a cationic binding domain that attaches to the negatively charged DNA origami surface via electrostatic interactions. The protein is attached to dendron through cysteine-maleimide bond, making the modular approach highly versatile. This work demonstrates the coating using two different proteins: bovine serum albumin (BSA) and class II hydrophobin (HFBI). The results reveal that BSA-coating significantly improves the origami stability against endonucleases (DNase I) and enhances the transfection into human embryonic kidney (HEK293) cells. Importantly,it is observed that BSA-coating attenuates the activation of immune response in mouse primary splenocytes. Serum albumin is the most abundant protein in the blood with a long circulation half-life and has already found clinically approved applications in drug delivery. It is therefore envisioned that the proposed system can open up further opportunities to tune the properties of DNA nanostructures in biological environment, and enable their use in various delivery applications.

Cellular homeostasis of the minor spliceosome is regulated by a negative feed-back loop that targets U11-48K and U11/U12-65K mRNAs encoding essential components of the U12-type intron-specific U11/U12 di-snRNP. This involves interaction of the U11 snRNP with an evolutionarily conserved splicing enhancer giving rise to unproductive mRNA isoforms. In the case of U11/U12-65K, this mechanism controls the length of the 3′ untranslated region (3′UTR). We show that this process is dynamically regulated in developing neurons and some other cell types, and involves a binary switch between translation-competent mRNAs with a short 3′UTR to non-productive isoforms with a long 3′UTR that are retained in the nucleus or/and spliced to the downstream amylase locus. Importantly, the choice between these alternatives is determined by alternative terminal exon definition events regulated by conserved U12- and U2-type 5′ splice sites as well as sequence signals used for pre-mRNA cleavage and polyadenylation. We additionally show that U11 snRNP binding to the U11/U12-65K mRNA species with a long 3′UTR is required for their nuclear retention. Together, our studies uncover an intricate molecular circuitry regulating the abundance of a key spliceosomal protein and shed new light on the mechanisms limiting the export of non-productively spliced mRNAs from the nucleus to the cytoplasm., Author summary The cellular homeostasis of many components of the eukaryotic RNA processing machinery is regulated via negative feed-back pathways that result in the formation of both productive and non-productive mRNA species. Typically, the formation of non-productive mRNAs species results from changes in alternative splicing that disrupt the reading frame of the protein coding region and leads to destabilization of the mRNA. Here, we have investigated the homeostasis regulation of the U11/U12-65K mRNA that encodes an essential protein component of the minor (U12-dependent) spliceosome intron recognition complex. We show that homeostasis is regulated at the level of nuclear mRNA export and mRNA 3′-end formation, and that it can be further regulated during neuronal differentiation. We describe a multilayered regulatory system utilizing alternative exon definition interactions that use the input from both spliceosomes and the polyadenylation machinery to decide between productive and non-productive mRNA formation. Because the 65K protein is an essential component of the minor spliceosome, this regulatory pathway can potentially affect the expression of ~700 genes containing U12-type introns.

DNA origami structures can be programmed into arbitrary shapes with nanometer scale precision, which opens up numerous attractive opportunities to engineer novel functional materials. One intriguing possibility is to use DNA origamis for fully tunable, targeted, and triggered drug delivery. In this work, we demonstrate the coating of DNA origami nanostructures with virus capsid proteins for enhancing cellular delivery. Our approach utilizes purified cowpea chlorotic mottle virus capsid proteins that can bind and self-assemble on the origami surface through electrostatic interactions and further pack the origami nanostructures inside the viral capsid. Confocal microscopy imaging and transfection studies with a human HEK293 cell line indicate that protein coating improves cellular attachment and delivery of origamis into the cells by 13-fold compared to bare DNA origamis. The presented method could readily find applications not only in sophisticated drug delivery applications but also in organizing intracellular reactions by origami-based templates.

International audience; Germline mutations in the gene encoding tumor suppressor kinase LKB1 lead to gastrointestinal tumorigenesis in Peutz-Jeghers syndrome (PJS) patients and mouse models; however, the cell types and signaling pathways underlying tumor formation are unknown. Here, we demonstrated that mesenchymal progenitor- or stromal fibroblast-specific deletion of Lkb1 results in fully penetrant polyposis in mice. Lineage tracing and immunohistochemical analyses revealed clonal expansion of Lkb1-deficient myofibroblast-like cell foci in the tumor stroma. Loss of Lkb1 in stromal cells was associated with induction of an inflammatory program including IL-11 production and activation of the JAK/STAT3 pathway in tumor epithelia concomitant with proliferation. Importantly, treatment of LKB1-defcient mice with the JAK1/2 inhibitor ruxolitinib dramatically decreased polyposis. These data indicate that IL-11-mediated induction of JAK/STAT3 is critical in gastrointestinal tumorigenesis following Lkb1 mutations and suggest that targeting this pathway has therapeutic potential in Peutz-Jeghers syndrome.

A dinuclear pyridyl-bridged palladium complex, trans-(P,N)-[PdBr(μ- C5H4N-C2,N)(PPh3)]2 1, was obtained from material isolated from the Suzuki cross-coupling reaction of 2-bromopyridine with 2,4-difluorophenylboronic acid in the presence of catalytic (PPh3)4Pd. Complex 1 is an effective precatalyst for the Suzuki cross-coupling reactions of a variety organoboronic acids and aryl bromides, and represents a useful source of mono-ligated palladium(0), "(Ph3P)Pd(0)".

The removal of non-coding sequences, introns, from the mRNA precursors is an essential step in eukaryotic gene expression. U12-type introns are a minor subgroup of introns, distinct from the major or U2-type introns. U12-type introns are present in most eukaryotes but only account for less than 0.5% of all introns in any given genome. They are processed by a specific U12-dependent spliceosome, which is similar to, but distinct from, the major spliceosome. U12-type introns are spliced somewhat less efficiently than the major introns, and it is believed that this limits the expression of the genes containing such introns. Recent findings on the role of U12-dependent splicing in development and human disease have shown that it can also affect multiple cellular processes not directly related to the functions of the host genes of U12-type introns. At the same time, advances in understanding the regulation and phylogenetic distribution of the minor spliceosome are starting to shed light on how the U12-type introns and the minor spliceosome may have evolved. © 2012 John Wiley & Sons, Ltd.

Many splicing regulators bind to their own pre-mRNAs to induce alternative splicing that leads to formation of unstable mRNA isoforms. This provides an autoregulatory feedback mechanism that regulates the cellular homeostasis of these factors. We have described such an autoregulatory mechanism for two core protein components, U11-48K and U11/U12-65K, of the U12-dependent spliceosome. This regulatory system uses an atypical splicing enhancer element termed USSE (U11 snRNP-binding splicing enhancer), which contains two U12-type consensus 5' splice sites (5'ss). Evolutionary analysis of the USSE element from a large number of animal and plant species indicate that USSE sequence must be located 25-50 nt downstream from the target 3' splice site (3'ss). Together with functional evidence showing a loss of USSE activity when this distance is reduced and a requirement for RS-domain of U11-35K protein for 3'ss activation, our data suggests that U11 snRNP bound to USSE uses exon definition interactions for regulating alternative splicing. However, unlike standard exon definition where the 5'ss bound by U1 or U11 will be subsequently activated for splicing, the USSE element functions similarly as an exonic splicing enhancer and is involved only in upstream splice site activation but does not function as a splicing donor. Additionally, our evolutionary and functional data suggests that the function of the 5'ss duplication within the USSE elements is to allow binding of two U11/U12 di-snRNPs that stabilize each others' binding through putative mutual interactions.

The Sonogashira couplings of 4-bromo-6-methyl-2-pyrone ( 5 ) with phenylacetylene, mediated by Pd(PPh3)2Cl2 in the presence of a CuI co-catalyst, have been investigated in detail. The concentration of Pd dramatically influences the product yield, with lower Pd-loadings favouring higher conversions and purer cross-coupled product. A post reaction time-dependence in product conversion is seen in samples quenched solely on silica-gel (eluted with CH2Cl2). The effect is mirrored in reactions employing 4-nitro-bromobenzene ( 14 ) and to a lesser extent (E) and (Z)-ethyl 3-iodo-2-propenonate ( 16 ) under similar conditions. A more efficient quenching system (using excess dppe) has been developed to enable accurate determinations in product conversions. Alternatively, solvent and base (Et3N) removal in vacuo, or quench with saturated aqueous ammonium chloride, prevents further turnover in Sonogashira coupling. An ESI-MS study on samples eluted through silica was undertaken to probe the nature of the soluble Pd/Cu species. The Sonogashira cross-coupling of 4-chloro- and 6-chloro-2-pyrone ( 18 and 20 , respectively) has further been investigated. The former undergoes successful coupling, however the latter decomposes in polar aprotic and protic solvents under standard conditions, through a chlorine substitution process, making Pd-mediated reactions problematic.

U12-type introns are a rare class of nuclear introns that are removed by a dedicated U12-dependent spliceosome and are thought to regulate the expression of their target genes owing through their slower splicing reaction. Recent genome-wide studies on the splicing of U12-type introns are now providing new insights on the biological significance of this parallel splicing machinery. The new studies cover multiple different organisms and experimental systems, including human patient cells with mutations in the components of the minor spliceosome, zebrafish with similar mutations and various experimentally manipulated human cells and Arabidopsis plants. Here, we will discuss the potential implications of these studies on the understanding of the mechanism and regulation of the minor spliceosome, as well as their medical implications.

U12-type introns are a rare class of introns in the genomes of diverse eukaryotes. In the human genome, they number over 700. A subset of these introns has been shown to be spliced at a slower rate compared to the major U2-type introns. This suggests a rate-limiting regulatory function for the minor spliceosome in the processing of transcripts containing U12-type introns. However, both the generality of slower splicing and the subsequent fate of partially processed pre-mRNAs remained unknown. Here, we present a global analysis of the nuclear retention of transcripts containing U12-type introns and provide evidence for the nuclear decay of such transcripts in human cells. Using SOLiD RNA sequencing technology, we find that, in normal cells, U12-type introns are on average 2-fold more retained than the surrounding U2-type introns. Furthermore, we find that knockdown of RRP41 and DIS3 subunits of the exosome stabilizes an overlapping set of U12-type introns. RRP41 knockdown leads to slower decay kinetics of U12-type introns and globally upregulates the retention of U12-type, but not U2-type, introns. Our results indicate that U12-type introns are spliced less efficiently and are targeted by the exosome. These characteristics support their role in the regulation of cellular mRNA levels.

Nickel-titanium alloy (Nitinol) is a metallic biomaterial that has a unique thermal shape memory, superelasticity, and high damping properties. Nitinol is potentially very useful in orthopedic surgery, for example. At present, there are not enough confirmative biocompatibility data available on Nitinol. The aim of our study was to clarify the primary cytotoxicity and corrosion rate of Nitinol in human cell cultures. Comparisons were made with stainless steel (Stst), titanium (Ti), composite material (C), and control cultures with no test discs. Human osteoblasts (OB) and fibroblasts (FB) were incubated for 10 days with test discs of equal size, 6 x 7 mm. The cultures were photographed and the cells counted. Samples from culture media were collected on days 2, 4, 6, and 8, and the analysis of metals in the media was done using flameless atomic absorption spectrophotometry. The proliferation of FB was 108% (Nitinol), 134% (Ti) (p < 0.02), 107% (Stst), and 48% (C)(p < 0.0001) compared to the control cultures. The proliferation of OB was 101% (Nitinol), 100% (Ti), 105% (Stst), and 54% (C) (p < 0.025) compared to the controls. Initially, Nitinol released more nickel (129-87 micrograms/L) into the cell culture media than Stst (7 micrograms/L), but after 2 days the concentrations were about equal (23-5 micrograms/L versus 11-1 micrograms/L). The titanium concentrations from both Nitinol and Ti samples were all < 20 micrograms/L. We conclude that Nitinol has good in vitro biocompatibility with human osteoblasts and fibroblasts. Despite the higher initial nickel dissolution, Nitinol induced no toxic effects, decrease in cell proliferation, or inhibition on the growth of cells in contact with the metal surface.

On following the kinetics of the Sonogashira alkynylation reaction of halogenated 2-pyrone 1 with phenylacetylene we have found that turnover continues to occur in sample vials even after quenching by commonly employed silica adsorption methods and product elution with small quantities of CH 2 Cl 2 . Trace quantities of Pd are carried through the silica plug. Addition of a CH 2 Cl 2 solution of 1,2-bis(diphenylphosphino)ethane (dppe) to the quenched sample inhibits the reaction and represents a more reliable method for determining yields and reaction kinetics.

Alternative pre-mRNA splicing is typically regulated by specific protein factors that recognize unique sequence elements in pre-mRNA and affect, directly or indirectly, nearby splice site usage. We show that 5' splice site sequences (5'ss) of U12-type introns, when repeated in tandem, form a U11 snRNP-binding splicing enhancer, USSE. Binding of U11 to the USSE regulates alternative splicing of U2-type introns by activating an upstream 3'ss. The U12-type 5'ss-like sequences within the USSE have a regulatory role and do not function as splicing donors. USSEs, present both in animal and plant genes encoding the U11/U12 di-snRNP-specific 48K and 65K proteins, create sensitive switches that respond to intracellular levels of functional U11 snRNP and alter the stability of 48K and 65K mRNAs. We conclude that U11 functions not only in 5'ss recognition in constitutive splicing, but also as an activator of U2-dependent alternative splicing and as a regulator of the U12-dependent spliceosome.

Its shape memory effect, superelasticity, and good wear and damping properties make the NiTi shape memory alloy a material with fascinating potential for orthopedic surgery. It provides a possibility for making self-locking, self-expanding, and self-compressing implants. Problems, however, may arise because of its high nickel content. The purpose of this work was to determine the corrosion of NiTi in vivo and to evaluate the possible deleterious effects of NiTi on osteotomy healing, bone mineralization, and the remodeling response. Femoral osteotomies of 40 rats were fixed with either NiTi or stainless steel (StSt) intramedullary nails. The rats were killed at 2, 4, 8, 12, 26, and 60 weeks. Bone healing was examined with radiographs, peripheral quantitative computed tomography, (pQCT) and histologically. The corrosion of the retrieved implants was analyzed by electron microscopy (FESEM). Trace metals from several organs were determined by graphite furnace atomic absorption spectrometry (GF-AAS) or by inductively coupled plasma-atomic emission spectrometry (ICP-AES). There were more healed bone unions in the NiTi than in the StSt group at early (4 and 8 weeks) time points. Callus size was equal between the groups. The total and cortical bone mineral densities did not differ between the NiTi and StSt groups. Mineral density in both groups was lower in the osteotomy area than in the other areas along the nail. Density in the nail area was lower than in the proximal part of the operated femur or the contralateral femur. Bone contact to NiTi was close. A peri-implant lamellar bone sheet formed in the metaphyseal area after 8 weeks, indicating good tissue tolerance. The FESEM assessment showed surface corrosion changes to be more evident in the StSt implants. There were no statistically significant differences in nickel concentration between the NiTi and StSt groups in any of the organs. NiTi appears to be an appropriate material for further intramedullary use because it has good biocompatibility in bone tissue.

Nickel-titanium shape memory alloy (Nitinol) has properties that could be very useful in surgical applications. Thermal shape memory, superelasticity, and high damping properties make such alloys behave differently compared to other implant metals. There has previously been a lack of sufficient evidence on the biocompatibility of Nitinol. The purpose of this study was to evaluate general soft tissue response and biocompatibility to Nitinol in vivo, and to clarify neural and perineural responses, previously unreported. Seventy-five rats were randomized into three groups. Test specimens were implanted into paravertebral muscle and near the sciatic nerve. A comparison was made between Nitinol, stainless steel, and Ti-6Al-4V. The animals were euthanized at 2, 4, 8, 12, and 26 weeks after implantation. General morphologic and histologic observations were made under light microscopy. Semiautomatic computerized image analysis was used to measure the encapsule membrane thickness around the implants. The muscular tissue response to Nitinol was clearly nontoxic, regardless of the time period. The overall inflammatory response to Nitinol was very similar to that of stainless steel and Ti-6Al-4V alloy. There were no necroses, granulomas, or signs of dystrophic soft tissue clacification. The immune cell response to Nitinol remained low. Only a few foreign-body giant cells were present. The detected neural and perineural responses were also clearly nontoxic and nonirritating with Nitinol. No qualitative differences in histology between the different test materials could be seen. At 8 weeks, the encapsule membrane of Nitinol was thicker than that of stainless steel (mean 62 +/- 25 microns vs. 41 +/- 8 microns). At the end of the study, the encapsule thickness was equal to all the materials tested. We concluded that Nitinol had good in vivo biocompatibility after intramuscular and perineural implantation in rats in the 26-week follow-up. Based on the results of the present study, Nitinol appears to have good potential for clinical use.