Nonsense-mediated mRNA decay efficiency varies in choroideremia providing a target to boost small molecule therapeutics

Choroideremia (CHM) is an x-linked recessive chorioretinal dystrophy, with 30% caused by nonsense mutations in the CHM gene resulting in an in-frame premature termination codon (PTC). Nonsense mediated decay (NMD) is the cell's natural surveillance mechanism, that detects and destroys PTC containing transcripts, with UPF1 being the central NMD modulator. NMD efficiency can be variable amongst individuals with some transcripts escaping destruction, leading to the production of a truncated non-functional or partially functional protein. Nonsense suppression drugs, such as ataluren, target these transcripts and read-through the PTC, leading to the production of a full length functional protein. Patients with higher transcript levels are considered to respond better to these drugs, as more substrate is available for read-through. Using RT-qPCR, we show that CHM mRNA expression in blood from nonsense mutation CHM patients is 2.8-fold lower than controls, and varies widely amongst patients, with 40% variation between those carrying the same UGA mutation (c.715 C > T; p.[R239*]). These results indicate that although NMD machinery is at work, efficiency is highly variable and not wholly dependent on mutation position. No significant difference in CHM mRNA levels was seen between two patients' fibroblasts and their iPSC-derived RPE. There was no correlation between CHM mRNA expression and genotype, phenotype or UPF1 transcript levels. NMD inhibition with caffeine was shown to restore CHM mRNA transcripts to near wildtype levels. Baseline mRNA levels may provide a prognostic indicator for response to nonsense suppression therapy, and caffeine may be a useful adjunct to enhance treatment efficacy where indicated

Insight into the relationship between the cell culture model, cell trafficking and siRNA silencing efficiency

Despite research efforts, cell uptake processes determining siRNA silencing efficiency remain unclear. Here, we examine the relationship between in vitro cell culture models, cellular trafficking and siRNA silencing efficiency to provide a mechanistic insight on siRNA delivery system design. Model siRNA-polyplexes, based on chitosan as a ‘classical’ condensing agent, were applied to a panel of lung epithelial cell lines, H1299, A549 and Calu-3 and cell internalization levels, trafficking pathways and gene silencing assessed on exposure to pharmacological inhibitors. The data reveal striking differences in the internalization behaviour and gene silencing efficiency in the tested cell lines, despite their common lung epithelial origins. The model system’s silencing was lower where clathrin internalization pathway predominated in Calu-3, relative to silencing in H1299 cells where a non-clathrin internalization appears dominant. Increased silencing on endosomal disruption was apparent in Calu-3 cells, but absent when cellular internalization was not predominantly clathrin-mediated in A549 cells. This highlights that identifying cell trafficking pathways before incorporation of functional components to siRNA delivery systems (e.g. endosomolytic compounds) is crucial. The study hence stresses the importance of selection of appropriate cell culture model, relevant to in vivo target, to assess the gene silencing efficiency and decide which functionalities the ‘stratified siRNA silencing vector’ requires

Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation.

Cryptococcus neoformans is a pathogenic basidiomycetous yeast responsible for more than 600,000 deaths each year. It occurs as two serotypes (A and D) representing two varieties (i.e. grubii and neoformans, respectively). Here, we sequenced the genome and performed an RNA-Seq-based analysis of the C. neoformans var. grubii transcriptome structure. We determined the chromosomal locations, analyzed the sequence/structural features of the centromeres, and identified origins of replication. The genome was annotated based on automated and manual curation. More than 40,000 introns populating more than 99% of the expressed genes were identified. Although most of these introns are located in the coding DNA sequences (CDS), over 2,000 introns in the untranslated regions (UTRs) were also identified. Poly(A)-containing reads were employed to locate the polyadenylation sites of more than 80% of the genes. Examination of the sequences around these sites revealed a new poly(A)-site-associated motif (AUGHAH). In addition, 1,197 miscRNAs were identified. These miscRNAs can be spliced and/or polyadenylated, but do not appear to have obvious coding capacities. Finally, this genome sequence enabled a comparative analysis of strain H99 variants obtained after laboratory passage. The spectrum of mutations identified provides insights into the genetics underlying the micro-evolution of a laboratory strain, and identifies mutations involved in stress responses, mating efficiency, and virulence

Synthesis and activity of a novel inhibitor of nonsense-mediated mRNA decay

During efforts to prepare the known compound , a new tetracyclic compound, called , was prepared in six steps. This compound was found to have good activity as an inhibitor of nonsense-mediated mRNA decay

Analysis of the Genome and Transcriptome of Cryptococcus neoformans var. grubii Reveals Complex RNA Expression and Microevolution Leading to Virulence Attenuation

Cryptococcus neoformans is a pathogenic basidiomycetous yeast responsible for more than 600,000 deaths each year. It occurs as two serotypes (A and D) representing two varieties (i.e. grubii and neoformans, respectively). Here, we sequenced the genome and performed an RNA-Seq-based analysis of the C. neoformans var. grubii transcriptome structure. We determined the chromosomal locations, analyzed the sequence/structural features of the centromeres, and identified origins of replication. The genome was annotated based on automated and manual curation. More than 40,000 introns populating more than 99% of the expressed genes were identified. Although most of these introns are located in the coding DNA sequences (CDS), over 2,000 introns in the untranslated regions (UTRs) were also identified. Poly(A)-containing reads were employed to locate the polyadenylation sites of more than 80% of the genes. Examination of the sequences around these sites revealed a new poly(A)-site-associated motif (AUGHAH). In addition, 1,197 miscRNAs were identified. These miscRNAs can be spliced and/or polyadenylated, but do not appear to have obvious coding capacities. Finally, this genome sequence enabled a comparative analysis of strain H99 variants obtained after laboratory passage. The spectrum of mutations identified provides insights into the genetics underlying the micro-evolution of a laboratory strain, and identifies mutations involved in stress responses, mating efficiency, and virulence

Socializing One Health: an innovative strategy to investigate social and behavioral risks of emerging viral threats

In an effort to strengthen global capacity to prevent, detect, and control infectious diseases in animals and people, the United States Agency for International Development’s (USAID) Emerging Pandemic Threats (EPT) PREDICT project funded development of regional, national, and local One Health capacities for early disease detection, rapid response, disease control, and risk reduction. From the outset, the EPT approach was inclusive of social science research methods designed to understand the contexts and behaviors of communities living and working at human-animal-environment interfaces considered high-risk for virus emergence. Using qualitative and quantitative approaches, PREDICT behavioral research aimed to identify and assess a range of socio-cultural behaviors that could be influential in zoonotic disease emergence, amplification, and transmission. This broad approach to behavioral risk characterization enabled us to identify and characterize human activities that could be linked to the transmission dynamics of new and emerging viruses. This paper provides a discussion of implementation of a social science approach within a zoonotic surveillance framework. We conducted in-depth ethnographic interviews and focus groups to better understand the individual- and community-level knowledge, attitudes, and practices that potentially put participants at risk for zoonotic disease transmission from the animals they live and work with, across 6 interface domains. When we asked highly-exposed individuals (ie. bushmeat hunters, wildlife or guano farmers) about the risk they perceived in their occupational activities, most did not perceive it to be risky, whether because it was normalized by years (or generations) of doing such an activity, or due to lack of information about potential risks. Integrating the social sciences allows investigations of the specific human activities that are hypothesized to drive disease emergence, amplification, and transmission, in order to better substantiate behavioral disease drivers, along with the social dimensions of infection and transmission dynamics. Understanding these dynamics is critical to achieving health security--the protection from threats to health-- which requires investments in both collective and individual health security. Involving behavioral sciences into zoonotic disease surveillance allowed us to push toward fuller community integration and engagement and toward dialogue and implementation of recommendations for disease prevention and improved health security

Identification of inhibitors of nonsense-mediated mRNA decay (NMD) and use as a therapeutic approach for some genetic diseases

Le NMD (nonsense-mediated mRNA decay) est un mécanisme qui reconnaît et dégrade les ARNm portant un codon stop prématuré afin d’empêcher la synthèse de protéines tronquées qui pourraient avoir des effets néfastes pour la cellule ou tout simplement être non fonctionnelles. Cependant, dans un certain nombre de cas, selon la position du codon stop prématuré, la protéine tronquée qui serait synthétisée si le NMD n’existait pas, pourrait remplir complètement ou partiellement la fonction de la protéine sauvage. Il faut noter qu’un codon stop prématuré est retrouvé dans le gène responsable d’une pathologie dans un tiers des maladies génétiques et de nombreuses formes de cancer. Dans la plus grande majorité des cas, la maladie se développe non pas parce qu’une protéine tronquée non fonctionnelle ou instable est synthétisée, mais plutôt parce que le gène muté n’est pas exprimé du fait de l’intervention du NMD sur l’ARNm qui en dérive. Une nouvelle approche thérapeutique de ces maladies serait d’inhiber le NMD afin de permettre la synthèse de protéines tronquées fonctionnelles et sauver le phénotype clinique. Nous avons donc décidé de rechercher des inhibiteurs du mécanisme du NMD parmi des petites molécules chimiques. Pour cela, nous avons mis au point un système de criblage en culture cellulaire reliant l’efficacité du NMD dans une cellule avec une activité luciférase mesurable directement sur les cultures cellulaires, au moyen d’un luminomètre. A partir d’un premier criblage d’environ 1500 composés chimiques, nous avons identifié une nouvelle molécule capable d’inhiber efficacement le NMD. De façon intéressante, cette nouvelle molécule est capable également d’induire la synthèse de protéines entières à partir d’un ARNm portant un codon stop prématuré. Nous avons utilisé cet inhibiteur dans des expériences pour déterminer son potentiel thérapeutique sur des modèles cellulaires de maladies génétiques tels que la dystrophie musculaire de Duchenne, la mucoviscidose et le cancer. Nos résultats démontrent que l’inhibition du NMD peut être en effet envisagée comme une nouvelle approche thérapeutique pour des maladies causées par l’apparition d’une mutation non sens. Nous avons aussi identifié une autre molécule chimique capable d’inhiber le NMD et permettant de faire un lien entre efficacité du NMD et intégrité du cytosquelette.MRNAs harboring a premature termination codon are rapidly degraded by a mechanism called nonsense-mediated mRNA decay (NMD). NMD is a surveillance pathway that prevents the synthesis of truncated proteins that could be harmful for the cell or simply be non-functional. However in some cases, depending on the position of the premature stop codon, the truncated protein that would be synthesized if there were no NMD would be partially or fully as functional as the wild-type protein. It is noteworthy that premature termination codons are found in approximately one-third of inherited genetic disorders and several forms of cancer. In most of cases the disease arises not because a non-functional or unstable truncated protein is synthesized, but instead because the degradation of the transcript by NMD leads to complete loss of protein production. Therefore, NMD inhibition could be an interesting therapeutic approach in some cases of nonsense-related genetic diseases in which functional truncated proteins can restore the clinical phenotype. We decided to search for NMD inhibitors among thousands of small molecules. We developed a cell-based screening method which couples NMD efficiency into the cell to a luciferase activity that can be measured directly into cells by a luminometer. From a screening of approximately 1500 compounds, we have identified one molecule capable of efficiently inhibit NMD. Interestingly, this compound is also able to induce the synthesis of full-length proteins from an mRNA bearing a premature termination codon. We evaluated the therapeutic potential of this compound in different cellular models of genetic disorders such as Duchenne’s muscular dystrophy, cystic fibrosis and cancer. Our results demonstrate that NMD inhibition in general can be considered as an useful therapeutic approach to rescue PTC consequences in genetic diseases provoked by the apparition of a nonsense mutation. We have also identified another compound that inhibits NMD and uncovers a relationship between the NMD efficiency and the integrity of the cytoskeleton

Identification d’inhibiteurs du nonsense-mediated mRNA decay (NMD) et utilisation comme approche thérapeutique dans certaines maladies génétiques

MRNAs harboring a premature termination codon are rapidly degraded by a mechanism called nonsense-mediated mRNA decay (NMD). NMD is a surveillance pathway that prevents the synthesis of truncated proteins that could be harmful for the cell or simply be non-functional. However in some cases, depending on the position of the premature stop codon, the truncated protein that would be synthesized if there were no NMD would be partially or fully as functional as the wild-type protein. It is noteworthy that premature termination codons are found in approximately one-third of inherited genetic disorders and several forms of cancer. In most of cases the disease arises not because a non-functional or unstable truncated protein is synthesized, but instead because the degradation of the transcript by NMD leads to complete loss of protein production. Therefore, NMD inhibition could be an interesting therapeutic approach in some cases of nonsense-related genetic diseases in which functional truncated proteins can restore the clinical phenotype. We decided to search for NMD inhibitors among thousands of small molecules. We developed a cell-based screening method which couples NMD efficiency into the cell to a luciferase activity that can be measured directly into cells by a luminometer. From a screening of approximately 1500 compounds, we have identified one molecule capable of efficiently inhibit NMD. Interestingly, this compound is also able to induce the synthesis of full-length proteins from an mRNA bearing a premature termination codon. We evaluated the therapeutic potential of this compound in different cellular models of genetic disorders such as Duchenne’s muscular dystrophy, cystic fibrosis and cancer. Our results demonstrate that NMD inhibition in general can be considered as an useful therapeutic approach to rescue PTC consequences in genetic diseases provoked by the apparition of a nonsense mutation. We have also identified another compound that inhibits NMD and uncovers a relationship between the NMD efficiency and the integrity of the cytoskeleton.Le NMD (nonsense-mediated mRNA decay) est un mécanisme qui reconnaît et dégrade les ARNm portant un codon stop prématuré afin d’empêcher la synthèse de protéines tronquées qui pourraient avoir des effets néfastes pour la cellule ou tout simplement être non fonctionnelles. Cependant, dans un certain nombre de cas, selon la position du codon stop prématuré, la protéine tronquée qui serait synthétisée si le NMD n’existait pas, pourrait remplir complètement ou partiellement la fonction de la protéine sauvage. Il faut noter qu’un codon stop prématuré est retrouvé dans le gène responsable d’une pathologie dans un tiers des maladies génétiques et de nombreuses formes de cancer. Dans la plus grande majorité des cas, la maladie se développe non pas parce qu’une protéine tronquée non fonctionnelle ou instable est synthétisée, mais plutôt parce que le gène muté n’est pas exprimé du fait de l’intervention du NMD sur l’ARNm qui en dérive. Une nouvelle approche thérapeutique de ces maladies serait d’inhiber le NMD afin de permettre la synthèse de protéines tronquées fonctionnelles et sauver le phénotype clinique. Nous avons donc décidé de rechercher des inhibiteurs du mécanisme du NMD parmi des petites molécules chimiques. Pour cela, nous avons mis au point un système de criblage en culture cellulaire reliant l’efficacité du NMD dans une cellule avec une activité luciférase mesurable directement sur les cultures cellulaires, au moyen d’un luminomètre. A partir d’un premier criblage d’environ 1500 composés chimiques, nous avons identifié une nouvelle molécule capable d’inhiber efficacement le NMD. De façon intéressante, cette nouvelle molécule est capable également d’induire la synthèse de protéines entières à partir d’un ARNm portant un codon stop prématuré. Nous avons utilisé cet inhibiteur dans des expériences pour déterminer son potentiel thérapeutique sur des modèles cellulaires de maladies génétiques tels que la dystrophie musculaire de Duchenne, la mucoviscidose et le cancer. Nos résultats démontrent que l’inhibition du NMD peut être en effet envisagée comme une nouvelle approche thérapeutique pour des maladies causées par l’apparition d’une mutation non sens. Nous avons aussi identifié une autre molécule chimique capable d’inhiber le NMD et permettant de faire un lien entre efficacité du NMD et intégrité du cytosquelette

The second bovine β-galactoside-α2,6-sialyltransferase (ST6Gal II): genomic organization and stimulation of its in vitro expression by IL-6 in bovine mammary epithelial cells

Chantier qualité GAWe have cloned a cDNA sequence encoding the second bovine β-galactoside-α2,6-sialyltransferase whose sequence shares more than 75% of identity with hST6Gal II cDNA coding sequence. The bovine gene, located on BTA 11, spans over 50 kbp with five exons (E1–E5) containing the 1488 bp open reading frame and a 5′-untranslated exon (E0). The gene expression pattern reveals a specific tissue distribution (brain, lungs, spleen, salivary, and mammary glands) compared to ST6Gal I which is ubiquitously expressed. We identified for bovine ST6Gal II three kinds of transcripts which differ by their 5′-untranslated regions. Among them, two transcripts are brain specific whereas the third one is found in all of the tissues expressing the gene. Two pFlag-bST6Gal II vector constructions were separately transfected in COS-1 cells in order to express either membrane-bound or soluble active forms of ST6Gal II. Enzymatic assays with these two forms indicated that the enzyme used the LacdiNAc structure (GalNAcβ1,4GlcNAc) as a better acceptor substrate than the Type II (Galβ1-4GlcNAc) disaccharide. Moreover, the enzyme's efficiency is improved when the acceptor substrate is provided as a free oligosaccharide rather than as a protein-bound oligosaccharide. In order to investigate the potential role of ST6Gal II during the acute phase of inflammation, we used primary cultures of bovine mammary epithelial cells which were stimulated with pro-inflammatory cytokines. It appears that the ST6Gal II gene was upregulated in cells stimulated by IL-6. This result suggested that α2,6-sialylation mediated by this gene could contribute to organism's response to infections