An improved SNAP-ADAR tool enables efficient RNA base editing to interfere with post-translational protein modification.

RNA base editing relies on the introduction of adenosine-to-inosine changes into target RNAs in a highly programmable manner in order to repair disease-causing mutations. Here, we propose that RNA base editing could be broadly applied to perturb protein function by removal of regulatory phosphorylation and acetylation sites. We demonstrate the feasibility on more than 70 sites in various signaling proteins and identify key determinants for high editing efficiency and potent down-stream effects. For the JAK/STAT pathway, we demonstrate both, negative and positive regulation. To achieve high editing efficiency over a broad codon scope, we applied an improved version of the SNAP-ADAR tool. The transient nature of RNA base editing enables the comparably fast (hours to days), dose-dependent (thus partial) and reversible manipulation of regulatory sites, which is a key advantage over DNA (base) editing approaches. In summary, PTM interference might become a valuable field of application of RNA base editing.

Pho1a (plastid starch phosphorylase) is duplicated and essential for normal starch granule phenotype in tubers of Solanum tuberosum L.

Reserve starch from seeds and tubers is a crucial plant product for human survival. Much research has been devoted to quantitative and qualitative aspects of starch synthesis and its relation to abiotic factors of importance in agriculture. Certain aspects of genetic factors and enzymes influencing carbon assimilation into starch granules remain elusive after many decades of research. Starch phosphorylase (Pho) can operate, depending on metabolic conditions, in a synthetic and degradative pathway. The plastidial form of the enzyme is one of the most highly expressed genes in potato tubers, and the encoded product is imported into starch-synthesizing amyloplasts. We identified that the genomic locus of a Pho1a-type starch phosphorylase is duplicated in potato. Our study further shows that the enzyme is of importance for a normal starch granule phenotype in tubers. Null mutants created by genome editing display rounded starch granules in an increased number that contained a reduced ratio of apparent amylose in the starch.

CLUSTER guide RNAs enable precise and efficient RNA editing with endogenous ADAR enzymes in vivo.

RNA base editing represents a promising alternative to genome editing. Recent approaches harness the endogenous RNA-editing enzyme adenosine deaminase acting on RNA (ADAR) to circumvent problems caused by ectopic expression of engineered editing enzymes, but suffer from sequence restriction, lack of efficiency and bystander editing. Here we present in silico-optimized CLUSTER guide RNAs that bind their target messenger RNAs in a multivalent fashion, achieve editing with high precision and efficiency and enable targeting of sequences that were not accessible using previous gRNA designs. CLUSTER gRNAs can be genetically encoded and delivered using viruses, and are active in a wide range of cell lines. In cell culture, CLUSTER gRNAs achieve on-target editing of endogenous transcripts with yields of up to 45% without bystander editing. In vivo, CLUSTER gRNAs delivered to mouse liver by hydrodynamic tail vein injection edited reporter constructs at rates of up to 10%. The CLUSTER approach opens avenues for drug development in the field of RNA base editing.

Precise RNA editing by recruiting endogenous ADARs with antisense oligonucleotides.

Site-directed RNA editing might provide a safer or more effective alternative to genome editing in certain clinical scenarios. Until now, RNA editing has relied on overexpression of exogenous RNA editing enzymes or of endogenous human ADAR (adenosine deaminase acting on RNA) enzymes. Here we describe the engineering of chemically optimized antisense oligonucleotides that recruit endogenous human ADARs to edit endogenous transcripts in a simple and programmable way, an approach we call RESTORE (recruiting endogenous ADAR to specific transcripts for oligonucleotide-mediated RNA editing). We observed almost no off-target editing, and natural editing homeostasis was not perturbed. We successfully applied RESTORE to a panel of standard human cell lines and human primary cells and demonstrated repair of the clinically relevant PiZZ mutation, which causes α1-antitrypsin deficiency, and editing of phosphotyrosine 701 in STAT1, the activity switch of the signaling factor. RESTORE requires only the administration of an oligonucleotide, circumvents ectopic expression of proteins, and represents an attractive approach for drug development.

Critical review on engineering deaminases for site-directed RNA editing.

The game-changing role of CRISPR/Cas for genome editing draw interest to programmable RNA-guided tools in general. Currently, we see a wave of papers pioneering the CRISPR/Cas system for RNA targeting, and applying them for site-directed RNA editing. Here, we exemplarily compare three recent RNA editing strategies that rely on three distinct RNA targeting mechanisms. We conclude that the CRISPR/Cas system seems not generally superior to other RNA targeting strategies in solving the most pressing problem in the RNA editing field, which is to obtain high efficiency in combination with high specificity. However, once achieved, RNA editing promises to complement or even outcompete DNA editing approaches in therapy, and also in some fields of basic research.

Efficient and precise editing of endogenous transcripts with SNAP-tagged ADARs.

Molecular tools that target RNA at specific sites allow recoding of RNA information and processing. SNAP-tagged deaminases guided by a chemically stabilized guide RNA can edit targeted adenosine to inosine in several endogenous transcripts simultaneously, with high efficiency (up to 90%), high potency, sufficient editing duration, and high precision. We used adenosine deaminases acting on RNA (ADARs) fused to SNAP-tag for the efficient and concurrent editing of two disease-relevant signaling transcripts, KRAS and STAT1. We also demonstrate improved performance compared with that of the recently described Cas13b-ADAR.

Effect of inhaled nitric oxide on oxygen therapy, mechanical ventilation, and hypoxic respiratory failure.

To assess the role of inhaled nitric oxide (iNO) in reducing the need for oxygen therapy, decreasing time on mechanical ventilatory support, and attenuating probability of hypoxic respiratory failure severity progression, we reviewed published reports of phase III iNO studies in neonates with hypoxic respiratory failure and pulmonary hypertension, as well as a novel post-hoc analysis of data from the Clinical Inhaled Nitric Oxide Research Group Initiative (CINRGI) study population not been previously reported. The post-hoc analysis of the CINRGI study showed that iNO shortens the duration of oxygen therapy versus placebo (17 vs. 34 days; P<0.05); the CINRGI retrospective analysis by Konduri et al. showed earlier administration of iNO (oxygenation index [OI] 15-25) yielded a 48% relative reduction vs. placebo in number of patients who progressed to OI≥30 (16.7% vs. 32.2%; P=0.002). Golombek and Young's pooled analysis of phase III studies showed a rapid improvement in oxygenation after initiation of iNO therapy versus controls in each study, and a significant reduction in median ventilation duration (11 vs. 14 days; P=0.003). A study by Gonzalez et al. revealed that earlier iNO administration in infants with mild to moderate hypoxic respiratory failure (OI 10-30) resulted in a decreased duration of oxygen therapy versus placebo (11.5 vs. 18.0 days; P<0.03) and reduced the probability of developing severe hypoxic respiratory failure.

Switching Protein Localization by Site-Directed RNA Editing under Control of Light.

Site directed RNA editing is an engineered tool for the posttranscriptional manipulation of RNA and proteins. Here, we demonstrate the inclusion of additional N- and C-terminal protein domains in an RNA editing-dependent manner to switch between protein isoforms in mammalian cell culture. By inclusion of localization signals, a switch of the subcellular protein localization was achieved. This included the shift from the cytoplasm to the outer-membrane, which typically is inaccessible at the protein-level. Furthermore, the strategy allows to implement photocaging to achieve spatiotemporal control of isoform switching. The strategy does not require substantial genetic engineering, and might well complement current optogenetic and optochemical approaches.

The notorious R.N.A. in the spotlight - drug or target for the treatment of disease.

mRNA is an attractive drug target for therapeutic interventions. In this review we highlight the current state, clinical trials, and developments in antisense therapy, including the classical approaches like RNaseH-dependent oligomers, splice-switching oligomers, aptamers, and therapeutic RNA interference. Furthermore, we provide an overview on emerging concepts for using RNA in therapeutic settings including protein replacement by in-vitro-transcribed mRNAs, mRNA as vaccines and anti-allergic drugs. Finally, we give a brief outlook on early-stage RNA repair approaches that apply endogenous or engineered proteins in combination with short RNAs or chemically stabilized oligomers for the re-programming of point mutations, RNA modifications, and frame shift mutations directly on the endogenous mRNA.

Site-Directed RNA Editing in Vivo Can Be Triggered by the Light-Driven Assembly of an Artificial Riboprotein.

Site-directed RNA editing allows for the manipulation of RNA and protein function by reprogramming genetic information at the RNA level. For this we assemble artificial RNA-guided editases and demonstrate their transcript repair activity in cells and in developing embryos of the annelid Platynereis dumerilii. A hallmark of our assembly strategy is the covalent attachment of guideRNA and editing enzyme by applying the SNAP-tag technology, a process that we demonstrate here to be readily triggered by light in vitro, in mammalian cell culture, and also in P. dumerilii. Lacking both sophisticated chemistry and extensive genetic engineering, this technology provides a convenient route for the light-dependent switching of protein isoforms. The presented strategy may also serve as a blue-print for the engineering of addressable machineries that apply tailored nucleic acid analogues to manipulate RNA or DNA site-specifically in living organisms.

Superoxide enhances Ca2+ entry through L-type channels in the renal afferent arteriole.

Reactive oxygen species regulate cardiovascular and renal function in health and disease. Superoxide participates in acute calcium signaling in afferent arterioles and renal vasoconstriction produced by angiotensin II, endothelin, thromboxane, and pressure-induced myogenic tone. Known mechanisms by which superoxide acts include quenching of nitric oxide and increased ADP ribosyl cyclase/ryanodine-mediated calcium mobilization. The effect(s) of superoxide on other calcium signaling pathways in the renal microcirculation is poorly understood. The present experiments examined the acute effect of superoxide generated by paraquat on calcium entry pathways in isolated rat afferent arterioles. The peak increase in cytosolic calcium concentration caused by KCl (40 mmol/L) was 99±14 nmol/L. The response to this membrane depolarization was mediated exclusively by L-type channels because it was abolished by nifedipine but was unaffected by the T-type channel blocker mibefradil. Paraquat increased superoxide production (dihydroethidium fluorescence), tripled the peak response to KCl to 314±68 nmol/L (P<0.001) and doubled the plateau response. These effects were abolished by tempol and nitroblue tetrazolium, but not by catalase, confirming actions of superoxide and not of hydrogen peroxide. Unaffected by paraquat and superoxide was calcium entry through store-operated calcium channels activated by thapsigargin-induced calcium depletion of sarcoplasmic reticular stores. Also unresponsive to paraquat was ryanodine receptor-mediated calcium-induced calcium release from the sarcoplasmic reticulum. Our results provide new evidence that superoxide enhances calcium entry through L-type channels activated by membrane depolarization in rat cortical afferent arterioles, without affecting calcium entry through store-operated entry or ryanodine receptor-mediated calcium mobilization.

Improving site-directed RNA editing in vitro and in cell culture by chemical modification of the guideRNA.

Adenosine-to-inosine deamination can be re-addressed to user-defined mRNAs by applying phosphothioate/2'-methoxy-modified guideRNAs. Dense chemical modification of the guideRNA clearly improves performance of the covalent conjugates inside the living cell. Furthermore, careful positioning of a few modifications controls editing selectivity in vitro and was exploited for the challenging repair of the Factor 5 Leiden missense mutation.

Site-directed RNA editing with antagomir deaminases--a tool to study protein and RNA function.

RNA-guided machineries perfectly satisfy the demand for rationally programmable tools that manipulate gene function inside the cell. Over the last ten years, various natural machineries have been harnessed, with RNA interference being among the most prominent examples. It is now time to tackle the engineering of novel RNA-guided tools not provided by nature. In this respect, we highlight RNA-guided site-directed RNA editing as a new concept for the manipulation of RNA and protein function. In contrast to currently available techniques, RNA editing allows for the introduction of selected point mutations into the transcriptome without the need for genomic manipulation. In particular, the approach described using chemically stabilized, antagomir-like guideRNAs may offer advantages over others, such as specificity and circumvention of immunogenicity. These new tools have significant potential for the advancement of both basic science and medicinal application, especially in the treatment of genetic diseases.

Thromboxane-induced renal vasoconstriction is mediated by the ADP-ribosyl cyclase CD38 and superoxide anion.

The present renal hemodynamic study tested the hypothesis that CD38 and superoxide anion (O2(·-)) participate in the vasoconstriction produced by activation of thromboxane prostanoid (TP) receptors in the mouse kidney. CD38 is the major mammalian ADP-ribosyl cyclase contributing to vasomotor tone through the generation of cADP-ribose, a second messenger that activates ryanodine receptors to release Ca(2+) from the sarcoplasmic reticulum in vascular smooth muscle cells. We evaluated whether the stable thromboxane mimetic U-46619 causes less pronounced renal vasoconstriction in CD38-deficient mice and the involvement of O2(·-) in U-46619-induced renal vasoconstriction. Our results indicate that U-46619 activation of TP receptors causes renal vasoconstriction in part by activating cADP-ribose signaling in renal resistance arterioles. Based on maximal renal blood flow and renal vascular resistance responses to bolus injections of U-46619, CD38 contributes 30-40% of the TP receptor-induced vasoconstriction. We also found that the antioxidant SOD mimetic tempol attenuated the magnitude of vasoconstriction by U-46619 in both groups of mice, suggesting mediation by O2(·-). The degree of tempol blockage of U-46619-induced renal vasoconstriction was greater in wild-type mice, attenuating renal vasoconstriction by 40% compared with 30% in CD38-null mice. In other experiments, U-46619 rapidly stimulated O2(·-) production (dihydroethidium fluorescence) in isolated mouse afferent arterioles, an effect abolished by tempol. These observations provide the first in vivo demonstration of CD38 and O2(·-) involvement in the vasoconstrictor effects of TP receptor activation in the kidney and in vitro evidence for TP receptor stimulation of O2(·-) production by the afferent arteriole.

C-peptide-stimulated nitric oxide production in a cultured pulmonary artery endothelium is erythrocyte mediated and requires Zn(2+).

BACKGROUND: C-peptide has been shown to stimulate the production of nitric oxide (NO) in aortic endothelial cells via activation of endothelial nitric oxide synthase (eNOS) through an increased calcium influx. Here, results obtained using cultured bovine pulmonary artery endothelial cells (bPAECs) suggest that C-peptide does not induce eNOS activation directly in cultured pulmonary artery endothelium. However, C-peptide has been shown to stimulate the release of ATP from erythrocytes, a well-documented stimulus of eNOS activity in the pulmonary endothelium. Therefore, studies were performed to examine if C-peptide can indirectly stimulate NO production in a cultured pulmonary endothelium that is erythrocyte mediated. METHODS: NO production and free intracellular calcium changes were monitored in immobilized bPAECs using specific intracellular fluorescent probes after stimulation with adenosine triphosphate (ATP), calcium ionophore A23187, or C-peptide. A microfluidic device enabled immobilized bPAECs to interact with flowing erythrocytes in the presence and absence of C-peptide to determine the role of the erythrocyte in C-peptide-stimulated NO production in cultured bPAECs. RESULTS: ATP and the calcium ionophore stimulate significant increases in both intracellular NO production and influx of free calcium in cultured bPAECs. In contrast, C-peptide, ranging from physiological to above physiological concentrations, was unable to stimulate NO production or calcium influx in the bPAECs. However, when erythrocytes were pre-incubated with a mixture containing physiological concentrations of C-peptide with Zn(2+) and haemodynamically pumped beneath bPAECs cultured on a microfluidic device, an 88.6 ± 7.5% increase in endothelial NO production was observed. CONCLUSIONS: C-peptide does not affect NO production in bPAECs directly but can impact NO production through an erythrocyte-mediated mechanism. Furthermore, in the absence of Zn(2+), C-peptide does not stimulate this NO production directly or indirectly. These results suggest that C-peptide, in the presence of Zn(2+), may be a determinant in purinergic receptor signalling via its ability to stimulate the release of ATP from erythrocytes.

Synthesis, structural, and photoluminescence studies of Gd(terpy)(H2O)(NO3)2M(CN)2 (M = Au, Ag) complexes: multiple emissions from intra- and intermolecular excimers and exciplexes.

The highly luminescent bimetallic cyanide materials, Gd(terpy)(H(2)O)(NO(3))(2)M(CN)(2) (M = Au, Ag; GdAu and GdAg, respectively) are quick and easy to synthesize under ambient conditions. A characteristic feature exhibited by both solid-state compounds is an intense red emission when excited with UV light. Additionally, GdAu exhibits a broad-band green emission upon excitation in the near UV region. A combination of structural and spectroscopic results for the compounds helps explain the underlying conditions responsible for their unique properties. Single-crystal X-ray diffraction experiments expose their structural features, including the fact that they are isostructural. Crystallographic data for the representative GdAu compound (Mo K(α), λ = 0.71073 Å, T = 290 K): triclinic, space group P ̅1, a = 7.5707(3) Å, b = 10.0671(4) Å, c = 15.1260(4) Å, α = 74.923(3)°, ß = 78.151(3)°, γ = 88.401(3)°, V = 1089.04(7) Å(3), and Z = 2. Although the compounds crystallize as dimers containing M···M distances smaller than the sum of their van der Waals radii, the Au···Au (3.5054(4) Å) and/or the Ag···Ag (3.6553(5) Å) interactions are relatively weak and are not responsible for the low energy red emission. Rather, the green emission in GdAu presumably originates from the [Au(CN)(2)(-)](2) dimeric excimer, while the [Ag(CN)(2)(-)](2) dimers in GdAg do not display visible emission at either 290 or 77 K. The unusual red emission exhibited by both compounds likely originates from the formation of an excited state exciplex that involves intermolecular π-stacking of 2,2':6',2"-terpyridine ligands. The room-temperature and low-temperature steady-state photoluminescent properties, along with detailed time-dependent, lifetime, and quantum yield spectroscopic data provide evidence regarding the sources of the multiple visible emissions exhibited by these complexes.

Microfluidic transendothelial electrical resistance measurement device that enables blood flow and postgrowth experiments.

Transendothelial electronic resistance (TEER) measurements are performed across a cell layer immobilized on a microfluidic device that also enables the cell layer to interact with a flowing stream of red blood cells (RBCs). A bipolar pulsed square wave potential is applied across a monolayer of bovine pulmonary artery endothelial cells, and the resulting current response is measured and integrated. The overall impedance of the cell layer provides an indicator of cell layer integrity. After cell seeding on the device, a decrease in TEER signal from 22.3 ± 1.6 µC to 3.5 ± 0.4 µC (corresponding to a resistance of 40.9 ± 2.9 Ω·cm(2) to 259.1 ± 27.4 Ω·cm(2)) was observed after 8 h of cell growth. Intracellular nitric oxide (NO) production by the immobilized endothelial cells that had reached confluence was 34% higher than those cells that had not reached confluence, as indicated by the integrated TEER system. Importantly, this NO production by the confluent endothelium was stimulated by ATP released from RBCs flowing under the endothelial cells. In this construct, the described microfluidic device enables both a TEER-based evaluation of cell layer integrity and molecularly communicated interactions of these cells with a flowing stream of blood components.