Functional classification of plant long noncoding RNAs: a transcript is known by the company it keeps.

The extraordinary maturation in high-throughput sequencing technologies has revealed the existence of a complex network of transcripts in eukaryotic organisms, including thousands of long noncoding (lnc) RNAs with little or no protein-coding capacity. Subsequent discoveries have shown that lncRNAs participate in a wide range of molecular processes, controlling gene expression and protein activity though direct interactions with proteins, DNA or other RNA molecules. Although significant advances have been achieved in the understanding of lncRNA biology in the animal kingdom, the functional characterization of plant lncRNAs is still in its infancy and remains a major challenge. In this review, we report emerging functional and mechanistic paradigms of plant lncRNAs and partner molecules, and discuss how cutting-edge technologies may help to identify and classify yet uncharacterized transcripts into functional groups.

Read-through circular RNAs reveal the plasticity of RNA processing mechanisms in human cells.

In the human genome, there are several genes whose primary transcripts are both canonically and non-canonically spliced to generate mRNAs and RNA circles, respectively. These RNA circles are a novel class of long non-coding RNAs that became known as circular RNAs (circRNAs). Recently, a new type of circRNA was discovered and called read-through circRNAs (rt-circRNAs). They are hybrid circles that include coding exons from two adjacent and similarly oriented genes. The function of rt-circRNAs, as well as the impact of read-through transcription in our transcriptome, remains to be elucidated. Although we have just begun to scratch it, here I discussed some insights that these fascinating circRNAs are already giving us about the plasticity of RNA processing in our cells.

Phase I and II clinical trials for the mucopolysaccharidoses.

INTRODUCTION: The mucopolysaccharidoses are lysosomal diseases characterized by deficient activity of one of the enzymes that degrades glycosaminoglycans. Treatment options are limited; therefore, new treatments are under investigation. Areas covered: We review the medicinal products for the treatment of mucopolysaccharidoses that are currently being investigated in phase I and phase II clinical trials. Expert opinion: The number of alternatives to treat MPS diseases increased dramatically in an attempt to provide therapy options for orphan MPS diseases and to address the unmet needs of the MPS that already have a treatment available. Intravenous enzyme replacement therapy (ERT) with fusion proteins, intrathecal/intracerebroventricular (ICV) ERT and gene therapy are the most promising strategies addressing the CNS manifestations. Stop-codon read-through, although proposed only for patients with nonsense mutations, might be useful in all MPS types. Substrate reduction therapy could also play a role in any MPS type, as anti-inflammatory drugs are also being tested. This new generation of therapies is now in clinical development and should bring new hope to MPS patients. As cost and logistics remain major challenges, especially for low- and middle-income countries, the possibility of having a one-time treatment such as gene therapy is anxiously awaited by affected families and healthcare systems.

Avances terapéuticos en errores innatos del metabolismo: pequeñas moléculas / Therapeutic advances in inborn errors of metabolism: small molecules

Resumen La mayoría de los Errores Innatos del Metabolismo (EIM) no tienen un tratamiento efectivo. Las terapias tradicionales tratan de reducir los sustratos, reemplazar el producto no formado, que puede ser esencial y suplementar con cofactores. También se emplea la activación de vías alternativas para la eliminación de productos intermedios tóxicos, como en el caso de los defectos del ciclo de la urea y para algunas condiciones, se dispone de la terapia de reemplazo enzimático (TRE), del trasplante de células hematopoyéticas y del trasplante hepático. En los últimos años se han desarrollado nuevas estrategias e caces para tratar estas enfermedades. Con esta revisión, se busca explicar de forma sencilla las distintas opciones terapéuticas más recientes, y en algunos casos, tratamientos prometedores para ciertos errores innatos de metabolismo (EIM). En concreto se hará referencia en primer lugar al uso terapéutico de pequeñas moléculas activas, que han surgido en las últimas dos décadas como un enfoque promisorio para el tratamiento de este heterogéneo grupo de trastornos, que incluyen terapia para restauración de la lectura, chaperonas farmacológicas, reguladores de la proteostasis, inhibidores de sustrato e inductores de autofagia. Estas pequeñas moléculas actúan en diferentes niveles celulares, y el conocimiento de los distintos procesos proporciona nuevas herramientas para establecer un tratamiento innovador.

Abstract Most Inborn Errors of Metabolism diseases do not have an effective treatment. Traditional therapies try to reduce substrates, replace non-formed product, which may be essential and supplement with cofactors. Activation of alternative routes for the disposal of toxic intermediates is also employed, as in the case of urea cycle defects for some conditions, enzyme replacement therapy (ERT), Hematopoietic Cell Transplantation and liver transplantation are available. In recent years new effective strategies have been developed to treat these diseases. This review seeks to explain in a simple way the different therapeutic options and, in some cases, promising treatments for certain inborn errors of metabolism (IEM). Specifically, reference will be made first to the therapeutic use of small active molecules, which have emerged in the last two decades as a promising approach for the treatment of this heterogeneous group of disorders, including: read-through therapy, pharmacological chaperones, protease inhibitors, substrate inhibitors and autophagy inducers. These small molecules act on different cellular levels, and the knowledge of the different processes provides new tools to establish an innovative treatment.

Small Molecules: Substrate Inhibitors, Chaperones, Stop-Codon Read Through, and Beyond

Abstract Lysosomal storage disorders are rare genetic disorders due to deficient lysosomal activity, which leads to progressive accumulation of nonmetabolized substrates. Patient's clinical outcomes have significantly improved since the advent of enzyme replacement therapy, even though this therapeutic approach presents important limitations, such as immune reactions, low bioavailability of recombinant enzymes, and incapability to reach the central nervous system. New strategies based on gene therapy or small molecules have been proposed and tested as an alternative to enzyme replacement therapy or to complement it. Small molecules are orally administrated, no antigenic compound that can diffuse across cell membranes and distribute in steady-state concentrations, also reaching the central nervous system. Substrate reduction therapy, pharmacological chaperones, and stop-codon read-through enhancers are small molecules currently available for the treatment of lysosomal storage disorders. This article describes the characteristics of this class of compounds and the possible strategies to improve their efficiency in future development.

A novel Werner Syndrome mutation: pharmacological treatment by read-through of nonsense mutations and epigenetic therapies.

Werner Syndrome (WS) is a rare inherited disease characterized by premature aging and increased propensity for cancer. Mutations in the WRN gene can be of several types, including nonsense mutations, leading to a truncated protein form. WRN is a RecQ family member with both helicase and exonuclease activities, and it participates in several cell metabolic pathways, including DNA replication, DNA repair, and telomere maintenance. Here, we reported a novel homozygous WS mutation (c.3767 C > G) in 2 Argentinian brothers, which resulted in a stop codon and a truncated protein (p.S1256X). We also observed increased WRN promoter methylation in the cells of patients and decreased messenger WRN RNA (WRN mRNA) expression. Finally, we showed that the read-through of nonsense mutation pharmacologic treatment with both aminoglycosides (AGs) and ataluren (PTC-124) in these cells restores full-length protein expression and WRN functionality.

Growing with the wind. Ribosomal protein hydroxylation and cell growth.

In this Extra View we comment on our recent work on Sudestada1 (Sud1), a Drosophila 2-oxoglutarate (2OG)-dependent dioxygenase that belongs to the Ribosomal Oxygenase (ROX) subfamily. Sud1 is required for normal growth in Drosophila, and is conserved in yeast and mammals. We reported that Sud1 hydroxylates the ribosomal protein S23 (RPS23), and that its loss of function restricts growth and provokes activation of the unfolded protein response, apoptosis and autophagy. In this Extra View we speculate on the role that RPS23 hydroxylation might play in stop codon recognition and on the possible link between Sud1 loss-of-function and activation of the Unfolded Protein Response, Stress Granules formation and growth impairment.