Large-scale analysis of small molecule-RNA interactions using multiplexed RNA structure libraries.

The large-scale analysis of small-molecule binding to diverse RNA structures is key to understanding the required interaction properties and selectivity for developing RNA-binding molecules toward RNA-targeted therapies. Here, we report a new system for performing the large-scale analysis of small molecule-RNA interactions using a multiplexed pull-down assay with RNA structure libraries. The system profiled the RNA-binding landscapes of G-clamp and thiazole orange derivatives, which recognizes an unpaired guanine base and are good probes for fluorescent indicator displacement (FID) assays, respectively. We discuss the binding preferences of these molecules based on their large-scale affinity profiles. In addition, we selected combinations of fluorescent indicators and different ranks of RNA based on the information and screened for RNA-binding molecules using FID. RNAs with high- and intermediate-rank RNA provided reliable results. Our system provides fundamental information about small molecule-RNA interactions and facilitates the discovery of novel RNA-binding molecules.

Large-Scale Analysis of RNA-Protein Interactions for Functional RNA Motif Discovery Using FOREST.

RNA transcripts can form a variety of higher-order structures. We developed a large-scale affinity analysis system, FOREST (Folded RNA Element Profiling with Structure Library), to investigate the function of these RNA structures on transcriptome-wide scale. Here we describe a protocol to analyze RNA-protein interactions using FOREST . Users of the protocol prepare an RNA structure library comprised of diverse species of transcripts and perform high-throughput characterization of the RNA-protein interactions to obtain quantitative and comprehensive information on the binding affinities and specificities. Moreover, we demonstrate how FOREST can be used to analyze a non-canonical structure, the RNA G-quadruplex, without sequencing bias, because the quantification is performed directly on a microarray without sequence amplification. FOREST will contribute to the discovery of RNA structure motifs that determine RNA-protein interactions.

Fluid flow-induced left-right asymmetric decay of Dand5 mRNA in the mouse embryo requires a Bicc1-Ccr4 RNA degradation complex.

Molecular left-right (L-R) asymmetry is established at the node of the mouse embryo as a result of the sensing of a leftward fluid flow by immotile cilia of perinodal crown cells and the consequent degradation of Dand5 mRNA on the left side. We here examined how the fluid flow induces Dand5 mRNA decay. We found that the first 200 nucleotides in the 3' untranslated region (3'-UTR) of Dand5 mRNA are necessary and sufficient for the left-sided decay and to mediate the response of a 3'-UTR reporter transgene to Ca2+, the cation channel Pkd2, the RNA-binding protein Bicc1 and their regulation by the flow direction. We show that Bicc1 preferentially recognizes GACR and YGAC sequences, which can explain the specific binding to a conserved GACGUGAC motif located in the proximal Dand5 3'-UTR. The Cnot3 component of the Ccr4-Not deadenylase complex interacts with Bicc1 and is also required for Dand5 mRNA decay at the node. These results suggest that Ca2+ currents induced by leftward fluid flow stimulate Bicc1 and Ccr4-Not to mediate Dand5 mRNA degradation specifically on the left side of the node.

RNA structure-wide discovery of functional interactions with multiplexed RNA motif library.

Biochemical assays and computational analyses have discovered RNA structures throughout various transcripts. However, the roles of these structures are mostly unknown. Here we develop folded RNA element profiling with structure library (FOREST), a multiplexed affinity assay system to identify functional interactions from transcriptome-wide RNA structure datasets. We generate an RNA structure library by extracting validated or predicted RNA motifs from gene-annotated RNA regions. The RNA structure library with an affinity enrichment assay allows for the comprehensive identification of target-binding RNA sequences and structures in a high-throughput manner. As a proof-of-concept, FOREST discovers multiple RNA-protein interaction networks with quantitative scores, including translational regulatory elements that function in living cells. Moreover, FOREST reveals different binding landscapes of RNA G-quadruplex (rG4) structures-binding proteins and discovers rG4 structures in the terminal loops of precursor microRNAs. Overall, FOREST serves as a versatile platform to investigate RNA structure-function relationships on a large scale.

Protein-driven RNA nanostructured devices that function in vitro and control mammalian cell fate.

Nucleic acid nanotechnology has great potential for future therapeutic applications. However, the construction of nanostructured devices that control cell fate by detecting and amplifying protein signals has remained a challenge. Here we design and build protein-driven RNA-nanostructured devices that actuate in vitro by RNA-binding-protein-inducible conformational change and regulate mammalian cell fate by RNA-protein interaction-mediated protein assembly. The conformation and function of the RNA nanostructures are dynamically controlled by RNA-binding protein signals. The protein-responsive RNA nanodevices are constructed inside cells using RNA-only delivery, which may provide a safe tool for building functional RNA-protein nanostructures. Moreover, the designed RNA scaffolds that control the assembly and oligomerization of apoptosis-regulatory proteins on a nanometre scale selectively kill target cells via specific RNA-protein interactions. These findings suggest that synthetic RNA nanodevices could function as molecular robots that detect signals and localize target proteins, induce RNA conformational changes, and programme mammalian cellular behaviour.Nucleic acid nanotechnology has great potential for future therapeutic applications. Here the authors build protein-driven RNA nanostructures that can function within mammalian cells and regulate the cell fate.

Monitoring and visualizing microRNA dynamics during live cell differentiation using microRNA-responsive non-viral reporter vectors.

MicroRNA (miRNA) activity differs with cell type, suggesting it can be used as a cell marker. In this study, we developed novel miRNA-responsive non-viral reporter vectors to continuously monitor and visualize miRNA dynamics during differentiation and to efficiently purify target living cells. Each vector codes miRNA-responsive and reference reporter genes in a single mRNA. These two genes are independent modules but transcribed by a single promoter, which enables us to distinguish miRNA-mediated post-transcriptional repression from transcriptional repression. We generated stable, miRNA-responsive vector-containing human induced pluripotent stem cells (hiPSCs) using the piggyBac transposon or episomal vectors. We could continuously monitor the differentiation status of living hiPSCs by detecting the activity of hiPSC-specific miRNA (miR-302a*). In addition, we could selectively sort hiPSC-derived cardiomyocytes using cardiomyocyte-specific miRNA (miR-208a or miR-1)-reporter vectors. Our miRNA reporter system provides a simple way to quantitatively and continuously monitor and visualize changes in the cellular state and should facilitate a broad range of studies that depend on cellular changes including drug discovery and cell-fate conversion.

Transbrachial intra-aortic balloon pumping for a patient with fulminant myocarditis.

A 57-year-old man with acute myocarditis was transferred to our hospital from a local clinic. The patient experienced unexpected sudden cardiac arrest 16 h after admission. Mechanical cardiopulmonary support was started using percutaneous cardiopulmonary support, intra-aortic balloon pumping (IABP), continuous hemodialysis filtration, and temporary cardiac pacing with percutaneous cannulation of the femoral vessels. Hematoma developed at the IABP insertion site on the 5th day after admission. The IABP was removed, and another IABP system was inserted via the left brachial artery. The patient's condition improved, and the IABP was removed on the 9th day after admission. The remainder of the patient's in-hospital treatment was uneventful, and he showed near-normal left ventricular systolic function 1 year after discharge.

Infective endocarditis associated with acute myocardial infarction caused by septic emboli.

A 53-year-old Japanese man presented with severe chest pain. He had suffered from persistent fever, muscle pain, arthralgia, and dyspnea on exertion (New York Heart Association class I) for two and half months prior to admission. He had been treated with several antibiotics for two months and prednisolone for almost one month prior to admission. On the day of admission, he had suffered from chest pain at rest, and had come to our hospital. Electrocardiography showed a normal sinus rhythm with significant ST segment elevation in leads V3-6 and abnormal Q waves in leads V4-6. Transthoracic echocardiography demonstrated left ventricular ejection fraction of 52% with severe mitral regurgitation and an 18-mm vegetation on the anterior mitral valve leaflet. Multiple blood cultures identified Streptococcus sanguis. The diagnosis was acute myocardial infarction and mitral regurgitation associated with infective endocarditis (IE). The incidence of acute coronary syndrome caused by IE is quite low in patients with native valves. After a 6-week course of antibiotics, mitral valve replacement and partial cardiomyotomy were performed. Two years after the surgery, follow-up echocardiography showed almost normal left ventricle function and no mitral regurgitation, and the patient has been living an active life without any complications.

Clinical characteristics of defecation syncope compared with micturition syncope.

BACKGROUND: Defecation syncope (DS) and micturition syncope (MS) are daily excretion-related syndromes that are both classified as situational. However, their clinical features seem to be very different, so the present comparative study aimed to clarify those of DS. METHODS AND RESULTS: The study population consisted of 20 consecutive patients with DS and 37 consecutive patients with MS. The DS patients were significantly older than the MS patients (63+/-15 vs 52+/-17 years, P=0.026). Gender was significantly different (P=0.026): women predominated in the DS group (60%) whereas men more commonly had MS (70%). The diurnal distribution of syncope differed (P=0.0054): 88% of MS episodes occurred between 6 pm and 6 am, whereas DS occurred almost equally throughout the 24 h. Syncope after drinking alcohol was less common with DS (10%) than with MS (60%) (P=0.0003), whereas gastrointestinal tract (GIT) symptoms as a premonitory sign were more common with DS (55%) than with MS (3%) (P<0.0001). Positive responses to head-up tilt testing did not differ between the DS and MS groups. CONCLUSIONS: DS tends to occur in elderly women and without any significant daily distribution. Alcohol-related syncope was uncommon in patients with DS, and preceding GIT symptoms may be important as predictors or triggering factors.

Prevalence of the Brugada-type electrocardiogram and incidence of Brugada syndrome in patients with sick sinus syndrome.

BACKGROUND: In the present study, clarification of the prevalence of the Brugada-type electrocardiogram (ECG) and the incidence of spontaneous ventricular fibrillation (VF) that occurred with the Brugada-type ECG in patients with sick sinus syndrome (SSS) was determined. METHODS AND RESULTS: A total of 487 consecutive patients (men 45%, mean age 69.9+/-12.3 years), who were defined as having an indication for cardiac pacemaker (PM) for SSS, were investigated. The ECG before an initial PM implantation and occurrence of VF or sudden cardiac death (SCD) was examined retrospectively. Brugada-type ECG was found in 14 patients (2.87%) including 4 (0.82%) with type 1 and 10 (2.05%) with type 2. During the follow-up period of 7.2+/-5.4 years, 2 out of the 4 patients with type 1 ECG had experienced a VF episode after the device implantation. In 10 patients with type 2 ECG, none had VF or SCD. The incidence of spontaneous VF (Brugada syndrome) in SSS patients was calculated as 14.1 per 100 person-years with type 1 ECG. CONCLUSIONS: The prevalence of typical Brugada-type (type 1) ECG in SSS patients seems to be higher compared with the general population. In addition, SSS patients with the typical Brugada-type ECG might be a high risk for spontaneous VF.

Hoarseness due to bilateral vocal cord paralysis as an initial manifestation of familial amyotrophic lateral sclerosis.

Bulbar palsy is unusual as an initial manifestation of amyotrophic lateral sclerosis (ALS), although common in the advanced stages. In terms of bulbar palsy as a presenting symptom, dysarthria and dysphagia are of common features. Hoarseness, however, is an initial symptom of ALS in only a small number of patients. We report a 43-year-old female with hoarseness due to bilateral vocal cord paralysis as the first manifestation of ALS. Gene analysis revealed a heterozygous missense mutation in the SOD1 gene, which resulted in an amino acid substitution of isoleucine 149 by threonine. Hoarseness can be the initial symptom of ALS. Therefore, in cases of bilateral vocal cord paralysis of unknown etiology, ALS should be taken into consideration.