Translation velocity determines the efficacy of engineered suppressor tRNAs on pathogenic nonsense mutations

Nonsense mutations - the underlying cause of approximately 11% of all genetic diseases - prematurely terminate protein synthesis by mutating a sense codon to a premature stop or termination codon (PTC). An emerging therapeutic strategy to suppress nonsense defects is to engineer sense-codon decoding tRNAs to readthrough and restore translation at PTCs. However, the readthrough efficiency of the engineered suppressor tRNAs (sup-tRNAs) largely varies in a tissue- and sequence context-dependent manner and has not yet yielded optimal clinical efficacy for many nonsense mutations. Here, we systematically analyze the suppression efficacy at various pathogenic nonsense mutations. We discover that the translation velocity of the sequence upstream of PTCs modulates the sup-tRNA readthrough efficacy. The PTCs most refractory to suppression are embedded in a sequence context translated with an abrupt reversal of the translation speed leading to ribosomal collisions. Moreover, modeling translation velocity using Ribo-seq data can accurately predict the suppression efficacy at PTCs. These results reveal previously unknown molecular signatures contributing to genotype-phenotype relationships and treatment-response heterogeneity, and provide the framework for the development of personalized tRNA-based gene therapies.

Engineered tRNAs suppress nonsense mutations in cells and in vivo

Nonsense mutations are the underlying cause of approximately 11% of all inherited genetic diseases1. Nonsense mutations convert a sense codon that is decoded by tRNA into a premature termination codon (PTC), resulting in an abrupt termination of translation. One strategy to suppress nonsense mutations is to use natural tRNAs with altered anticodons to base-pair to the newly emerged PTC and promote translation2-7. However, tRNA-based gene therapy has not yielded an optimal combination of clinical efficacy and safety and there is presently no treatment for individuals with nonsense mutations. Here we introduce a strategy based on altering native tRNAs into  efficient suppressor tRNAs (sup-tRNAs) by individually fine-tuning their sequence to the physico-chemical properties of the amino acid that they carry. Intravenous and intratracheal lipid nanoparticle (LNP) administration of sup-tRNA in mice restored the production of functional proteins with nonsense mutations. LNP-sup-tRNA formulations caused no discernible readthrough at endogenous native stop codons, as determined by ribosome profiling. At clinically important PTCs in the cystic fibrosis transmembrane conductance regulator gene (CFTR), the sup-tRNAs re-established expression and function in cell systems and patient-derived nasal epithelia and restored airway volume homeostasis. These results provide a framework for the development of tRNA-based therapies with a high molecular safety profile and high efficacy in targeted PTC suppression.

Repurposing tRNAs for nonsense suppression

Three stop codons (UAA, UAG and UGA) terminate protein synthesis and are almost exclusively recognized by release factors. Here, we design de novo transfer RNAs (tRNAs) that efficiently decode UGA stop codons in Escherichia coli. The tRNA designs harness various functionally conserved aspects of sense-codon decoding tRNAs. Optimization within the TΨC-stem to stabilize binding to the elongation factor, displays the most potent effect in enhancing suppression activity. We determine the structure of the ribosome in a complex with the designed tRNA bound to a UGA stop codon in the A site at 2.9 Å resolution. In the context of the suppressor tRNA, the conformation of the UGA codon resembles that of a sense-codon rather than when canonical translation termination release factors are bound, suggesting conformational flexibility of the stop codons dependent on the nature of the A-site ligand. The systematic analysis, combined with structural insights, provides a rationale for targeted repurposing of tRNAs to correct devastating nonsense mutations that introduce a premature stop codon.

Computational Aminoacyl-tRNA Synthetase Library Design for Photocaged Tyrosine

Engineering aminoacyl-tRNA synthetases (aaRSs) provides access to the ribosomal incorporation of noncanonical amino acids via genetic code expansion. Conventional targeted mutagenesis libraries with 5–7 positions randomized cover only marginal fractions of the vast sequence space formed by up to 30 active site residues. This frequently results in selection of weakly active enzymes. To overcome this limitation, we use computational enzyme design to generate a focused library of aaRS variants. For aaRS enzyme redesign, photocaged ortho-nitrobenzyl tyrosine (ONBY) was chosen as substrate due to commercial availability and its diverse applications. Diversifying 17 first- and second-shell sites and performing conventional aaRS positive and negative selection resulted in a high-activity aaRS. This MjTyrRS variant carries ten mutations and outperforms previously reported ONBY-specific aaRS variants isolated from traditional libraries. In response to a single in-frame amber stop codon, it mediates the in vivo incorporation of ONBY with an efficiency matching that of the wild type MjTyrRS enzyme acylating cognate tyrosine. These results exemplify an improved general strategy for aaRS library design and engineering.

Plasma concentrations of N-terminal brain natriuretic peptide in healthy children, adolescents, and young adults: effect of age and gender

Children with congenital heart disease need adequate diagnostic classification regarding their cardiovascular status (CVS). N-terminal brain natriuretic peptide (N-BNP) plasma concentration indicates dysfunction of the cardiovascular system and guides decisions concerning treatment and prognosis. Reference values are established for adults, with age-dependent increasing values and higher values in women. To avoid misclassification concerning the CVS, a large group of healthy children and adolescents can be used show the relationship between gender, age, and N-BNP and these can serve as reference values. N-BNP was measured in 434 healthy subjects (240 female and 194 male) with ages ranging from 0 to 32 years without any cardiovascular disease or renal or hepatic impairment. Measurements were performed with an electrochemiluminescence immunoassay from Roche Diagnostics. Mean N-BNP decreased from 12.6 fmol/ml (0-9 years; n = 79) to 9.41 fmol/ml (10-14 years; n = 154) and in adolescents from 6.1 (15-19 years; n = 99) to 4.8 fmol/ml (> 19 years; n = 102) in adults (p < 0.05). Mean N-BNP concerning gender did not differ in any age group younger than 19 years. In contrast, the adult female group had 78% higher N-BNP compared to the male group (p < 0.05). There was a significant peak in N-BNP at the age of 12-14 years. This study shows that reference values for N-BNP differed profoundly in children compared to adults and were up to 260% higher in children without any gender difference. Therefore, these reference values will help to avoid CVS misclassification in children for the biomarker N-BNP.

Genetic screening of newborns

Screening of newborn infants for genetic disease began over 35 years ago as a public health measure to prevent mental retardation in phenylketonuria (PKU). It was so successful that tests for several other genetic disorders were added. We review the current status of this screening, including discussions of the genetic disorders often covered and the results of newborn screening for them. We emphasize recent advances. These include expansion of coverage for genetic disorders with the new methodology of tandem mass spectrometry (MS-MS) and the introduction of molecular (DNA) testing to increase the specificity of testing for several disorders, thereby reducing false-positive rates. These and other advances have also produced issues of criteria for screening, missed cases, and appropriate use of stored newborn specimens.

Beneficial effects of alpha-lipoic acid and ascorbic acid on endothelium-dependent, nitric oxide-mediated vasodilation in diabetic patients: relation to parameters of oxidative stress

The impairment of nitric oxide (NO)-mediated vasodilation in diabetes has been attributed to increased vascular oxidative stress. Lipoic acid has been shown to have substantial antioxidative properties. The aim of this study was to assess the effect of lipoic acid on NO-mediated vasodilation in diabetic patients in comparison with the well-recognized effect of ascorbic acid. Using venous occlusion plethysmography, we examined the effects of lipoic acid (0.2 mM) and ascorbic acid (1 and 10 mM) on forearm blood flow responses to acetylcholine, sodium nitroprusside and concomitant infusion of the NO-inhibitor, N(G)-monomethyl-L-arginine, in 39 diabetic patients and 11 control subjects. Plasma levels of antioxidants and parameters of lipid peroxidation were measured and correlated to endothelial function tests. Lipoic acid improved NO-mediated vasodilation in diabetic patients, but not in controls. NO-mediated vasodilation was improved by ascorbic acid at 10 mM, but not 1 mM. Improvements of endothelial function by ascorbic acid and lipoic acid were closely related. The beneficial effects of lipoic acid were positively related to plasma levels of malondialdehyde and inversely related to levels of ubiquinol-10. These findings support the concept that oxidative stress contributes to endothelial dysfunction and suggest a therapeutic potential of lipoic acid particularly in patients with imbalance between increased oxidative stress and depleted antioxidant defense.

Detection of neonatal carnitine palmitoyltransferase II deficiency by expanded newborn screening with tandem mass spectrometry

The introduction of tandem mass spectrometry to newborn screening has substantially expanded our ability to diagnose metabolic diseases in the newborn period. We report the first case of neonatal carnitine palmitoyltransferase deficiency II detected by expanded newborn screening with tandem mass spectrometry. The neonate presented with dysmorphic facial features, structural malformations, renal failure, seizures, and cardiac arrythmias and died on the third day of life. This experience illustrates the importance of expanded newborn screening to avoid missing a metabolic diagnosis in early infantile death.

Tetrahydrobiopterin improves endothelium-dependent vasodilation by increasing nitric oxide activity in patients with Type II diabetes mellitus

AIMS/HYPOTHESIS

Tetrahydrobiopterin is an essential cofactor of nitric oxide synthase, and its deficiency decreases nitric oxide bioactivity. Our aim was to find whether supplementation of tetrahydrobiopterin could improve endothelial dysfunction in diabetic patients.

METHODS

Forearm blood flow responses to the endothelium-dependent vasodilator acetylcholine (0.75-3.0 microg x 100 ml(-1) x min(-1)) and to the endothelium-independent vasodilator sodium nitroprusside (0.1-1.0 microg x 100 ml(-1) x min(-1)) before and during concomitant intra-arterial infusion of tetrahydrobiopterin (500 microg/min) were measured by venous occlusion plethysmography in 12 control subjects and 23 patients with Type II (non-insulin-dependent) diabetes mellitus.

RESULTS

In control subjects, tetrahydrobiopterin had no effect on the dose-response curves to acetylcholine and sodium nitroprusside. In contrast, in diabetic patients, the attenuated endothelium-dependent vasodilation to acetylcholine was considerably improved by concomitant treatment with tetrahydrobiopterin, whereas the endothelium-independent vasodilation was not affected. This beneficial effect of tetrahydrobiopterin in diabetic patients could be completely blocked by N(G)-monomethyl-L-arginine.

CONCLUSION/INTERPRETATION

These findings suggest the possibility that endothelial dysfunction in Type II diabetes might be related to decreased availability of tetrahydrobiopterin.

Viruses, plasmids and other genetic elements of thermophilic and hyperthermophilic Archaea

We review and update the work on genetic elements, e.g., viruses and plasmids (exluding IS elements and transposons) in the kingdom Crenarchaeota (Thermoproteales and Sulfolobales) and the orders Thermococcales and Thermoplasmales in the kingdom Euryarchaeota of the archael domain, including unpublished data from our laboratory. The viruses of Crenarchaeota represent four novel virus families. The Fuselloviridae represented by SSVI of S. shibatae and relatives in other Sulfolobus strains have the form of a tailed spindle. The envelope is highly hydrophobic. The DNA is double-stranded and circular. Members of this group have also been found in Methanococcus and Haloarcula. The Lipothrivciridae (e.g., T TV1 to 3) have the form of flexible filaments. They have a core containing linear double-stranded DNA and DNA-binding proteins which is wrapped into a lipid membrane. The "Bacilloviridae" (e.g., TTV4 and SIRV) are stiff rods lacking this membrane, but also featuring linear double-stranded DNA and DNA-binding proteins. Both virus types carry on both ends structures involved in the attachment to receptors. Both types are represented in Thermoproteus and Sulfolobus. The droplet-formed novel Sulfolobus virus SNDV represents the "Guttaviridae" containing circular double-stranded DNA. Though head and tail viruses distantly resembling T phages or lambdoid phages were seen electronmicroscopically in solfataric water samples, no such virus has so far been isolated. SSV1 is temperate, TTV1 causes lysis after induction, the other viruses found so far exist in carrier states. The hosts of all but TTV1 survive virus production. We discuss the implications of the nature of these viruses for understanding virus evolution. The plasmids found so far range in size from 4.5 kb to about 40 kb. Most of them occur in high copy number, probably due to the way of their detection. Most are cryptic, pNOB8 is conjugative, the widespread pDL10 alleviates in an unknown way autotrophic growth of its host Desulfurolobus by sulfur reduction. The plasmid pTIK4 appears to encode a killer function. pNOB8 has been used as a vector for the transfer of the lac S (beta-galactosidase) gene into a mutant of S. solfataricus.

Prognostic significance of spontaneous motility in very immature preterm infants under intensive care treatment

Qualitative analysis of spontaneous motility was performed in 22 preterm infants (gestational age 25-31 weeks) on the intensive care unit. The infants were videorecorded once a week in the late afternoon during 1 h until 36 weeks of gestation. Quality of movement was analyzed by 8 observers using visual 'Gestalt perception' and compared with the neurological outcome 1 year after term. A normal quality of movement consistently predicted a normal neurological outcome with a probability of 90-100%. An abnormal quality of movement predicted an abnormal outcome with a probability of only 56% in the first, but with a probability of 82% in the third postnatal week. The average interobserver agreement was 78%. The analysis of spontaneous motility for the early diagnosis of neurological dysfunctions can reliably be applied on very immature preterms under intensive care conditions from the 3rd postnatal week on.

Glutamine-containing dipeptides in parenteral nutrition

Of the total pool of muscle free intracellular amino acids, glutamine represents about 60%. During catabolic stress, a marked reduction (50%) of this pool occurs; the depletion is not reversible by therapeutic efforts or conventional nutritional means. If maintenance of the intracellular glutamine pool promotes conservation of muscle protein, there is a theoretical case for use of glutamine supplements in the parenteral nutrition of patients with injury and infection. Glutamine is too unstable and poorly soluble for addition to existing preparations in its native form, but this drawback can be overcome by the use of synthetic stable and highly soluble glutamine-containing dipeptides. In vivo studies in humans and animals provide firm evidence that a synthetic glutamine-containing dipeptide, L-alanyl-L-glutamine (Ala-Gln), is readily hydrolyzed following its intravenous administration. The results also indicate a safe and efficient use of Ala-Gln as a source of free glutamine in parenteral nutrition. In clinical studies, nitrogen balance was more positive in catabolic patients receiving a peptide-supplemented solution than in control patients given isonitrogenous, isoenergetic total parenteral nutrition. Muscle glutamine concentrations were markedly decreased in the control groups. The intracellular concentrations were not influenced following severe injury, but were maintained in postoperative trauma. It is inferred that the increased intestinal requirement and cellular demand for metabolic fuel during catabolic stress is matched by an enhanced demand on muscle glutamine, resulting in intracellular glutamine depletion. Thus, the delivery of adequate amounts of glutamine is essential to maintain the integrity of intestinal mucosa and rapidly proliferating cells, to preserve the muscle glutamine pool, and to improve overall nitrogen economy during conditions of stress.

Evidence for a nutritional need for glutamine in catabolic patients

Of the total pool of muscle free intracellular amino acids, glutamine represents about 60%. During catabolic stress, a marked reduction (50%) of this pool occurs; the depletion is not reversible by nutrition or other therapeutical endeavors. Since free glutamine is unstable in solutions, the question is whether maintenance of this pool and improvement of the nitrogen economy is feasible by intravenous provision of synthetic, stable glutamine-containing dipeptides. In vivo studies in man and animals provide firm evidence that a synthetic glutamine containing dipeptide, L-alanyl-L-glutamine (Ala-Gln), is readily hydrolyzed following intravenous administration. The results also indicate a safe and efficient use of Ala-Gln as a source of free glutamine for parenteral nutrition. In clinical studies, nitrogen balance was more positive in catabolic patients receiving a peptide supplemented solution as compared with control patients given isonitrogenous, isoenergetic TPN. Preoperative muscle glutamine concentrations were essentially maintained in the peptide group and markedly decreased in the control group. It is inferred that the increased intestinal requirement of metabolic fuel during catabolic stress is matched by an enhanced demand on muscle glutamine, resulting in intracellular glutamine depletion. Thus, the delivery of adequate amounts of glutamine is essential to maintain the integrity of intestinal mucosa, to preserve the muscle glutamine pool, and to improve overall nitrogen economy during conditions of stress.

Availability of glutamine supplied intravenously as alanylglutamine

In this review, new knowledge about the potential use of glutamine containing dipeptides as substrates in the frame of parenteral nutrition is presented. Using chemical and biotechnological methods, the stable and highly soluble peptide L-alanyl-L-glutamine (Ala-Gln) can be synthesized in high yields. Studies in experimental rats and dogs demonstrate the effective utilization of intravenously supplied Ala-Gln and the rapid provision of free glutamine for maintenance of the intracellular muscle-free glutamine pool in catabolic situations. Subsequent studies in healthy volunteers provide firm evidence that the infused Ala-Gln is rapidly eliminated from plasma (t1/2:3.8 minutes), associated by a prompt equimolar increase in the concentrations of free alanine and glutamine. Bolus injection and continuous infusion of the peptide was not accompanied by any side effects, and no complaints by the subjects were noted. These results may indicate a safe and efficient use of Ala-Gln as source of free glutamine in parenteral nutrition.

Availability of amino acids supplied by constant intravenous infusion of synthetic dipeptides in healthy man

1. A commercial amino acid solution supplemented with two synthetic dipeptides, L-alanyl-L-glutamine (Ala-Gln) and glycyl-L-tyrosine (Gly-Tyr), or alternatively with isonitrogenous amounts of free alanine and glycine has been continuously infused over 4 h in six apparently healthy volunteers. 2. The infusion of the solutions was not accompanied by any side effects and the volunteers reported no complaints. 3. Infusion of the alanine- and glycine-supplemented control solution resulted in an increase of the concentration of these amino acids, while no appreciable change in free glutamine concentration was observed and free tyrosine revealed a steady decrease throughout the infusion. 4. Infusion of the peptide-supplemented solution resulted in a prompt equimolar liberation of the constituent free amino acids (glutamine, alanine, tyrosine and glycine), approaching steady state after about 30 min infusion, while only trace but stable concentrations of the two dipeptides were measured throughout the infusion. No peptides were detectable in urine. The findings suggest a nearly quantitative extracellular hydrolysis of the infused dipeptides and indicate a subsequent utilization of the liberated free amino acids. 5. The estimated metabolic clearance rates and total body plasma clearances were very similar for the two dipeptides (Ala-Gln 35.9 +/- 9.5 ml min-1 kg-1 and 2.9 +/- 0.9 l/min, respectively; Gly-Tyr 33.7 +/- 9.5 ml min-1 kg-1 and 2.7 +/- 0.9 l/min, respectively); thus there is little difference in the metabolic handling of these dipeptides.(ABSTRACT TRUNCATED AT 250 WORDS)

Effect of parenteral glutamine peptide supplements on muscle glutamine loss and nitrogen balance after major surgery

Twelve patients admitted for elective resection of carcinoma of colon or rectum were allocated at random to experimental and control groups (six in each) and received a total parenteral nutrition regimen providing 230 mg N/kg and 166 KJ/kg daily over the first 5 postoperative days. In the experimental group the parenteral fluid was supplemented with a synthetic glutamine-containing dipeptide, L-alanyl-L-glutamine (54 mg peptide-N/kg per day) and the control group received corresponding amounts of alanine-N and glycine-N. On each postoperative day nitrogen balance was better in the experimental group; mean daily nitrogen balance with alanyl-glutamine was -1.5 (SE 0.4) g N/day and with the control solution -3.6 (0.2) g N/day. The cumulative nitrogen balances on the fifth postoperative day were -7.1 (2.2) and -18.1 (1.7) g N, respectively. With the peptide-containing solution intramuscular glutamine concentration remained close to the preoperative value whereas with the control solution it decreased from 19.7 (SE 0.9) to 12.0 (0.6) mmol/l intracellular water.

In vivo utilization of cystine-containing synthetic short-chain peptides after intravenous bolus injection in the rat

For the first time, in vivo utilization of two highly soluble and stable cystine-containing synthetic short-chain peptides, bis-L-alanyl-L-cystine and bis-glycyl-L-cystine, were investigated in adult rats. Within 5 min after an intravenous bolus, blood samples were drawn (inferior vena cava) and plasma amino acid and peptide levels were determined using RP-HPLC (precolumn derivatization with 5-dimethylaminonaphthalene-1-sulfonylchloride). Both peptides were rapidly cleared from plasma (estimated elimination t1/2: 4 min for the glycyl peptide and less than 2 min for the alanyl peptide). The initial high amounts of mono-L-alanyl-L-cystine and mono-glycyl-L-cystine as well as the prompt increase of the constituent free amino acids alanine, glycine and cystine strongly suggest that the peptide disappearance is mainly due to a very fast two-step hydrolysis in the extracellular compartment, presumably catalyzed by soluble and/or plasma membrane-bound peptidases. The observed rapid hydrolysis may serve as first evidence that short-chain peptides with C-terminal cystine residue may represent efficient sources of free cystine in parenteral nutrition.

Availability of amino acids supplied intravenously in healthy man as synthetic dipeptides: kinetic evaluation of L-alanyl-L-glutamine and glycyl-L-tyrosine

1. For the first time utilization of intravenously administered L-alanyl-L-glutamine and glycyl-L-tyrosine was investigated by means of their kinetic behaviour after bolus injection in 10 and 11 apparently healthy male subjects (age 26.6 +/- 5.7 years), respectively. 2. The injection of the synthetic dipeptides was not accompanied by any side effects or complaints. 3. The synthetic dipeptides L-alanyl-L-glutamine and glycyl-L-tyrosine were rapidly cleared from plasma. By applying a monoexponential model the elimination half-lives were found to have very similar values (3.8 +/- 0.5 and 3.4 +/- 0.3 min) whether alanine or glycine was occupying the N-terminal position. The estimated volume of distribution was approximately that of the extracellular space. 4. Peptide disappearance was accompanied by a prompt equimolar increase in the concentrations of the constituent amino acids alanine and glutamine as well as glycine and tyrosine. 5. The study provides firm evidence that L-alanyl-L-glutamine and glycyl-L-tyrosine are rapidly (quantitatively) hydrolysed. The results of this study may indicate a safe and efficient parenteral use of the investigated peptides as sources of free glutamine and free tyrosine.

An ultra rapid and sensitive high-performance liquid chromatographic method for determination of tissue and plasma free amino acids

An ultra rapid and sensitive HPLC method for measuring individual free amino acids in biological fluids has been developed by using o-phthaldialdehyde/3-mercaptopropionic acid as derivatization agent and employing 3-micron-particle-size reversed-phase columns. Resolution of the amino acid derivatives is accomplished with an acetonitrile gradient in 12.5 mM sodium phosphate buffer, pH 7.2. These conditions facilitate separation of the 23 major tissue free physiological amino acids in the lower picomole range in less than 13 min. Muscle, liver, and kidney free amino acid concentrations, as determined by HPLC, are in the expected physiological range and compare favorably with those obtained by conventional amino acid analyzer.