Transcriptome-wide identification of NMD-targeted human mRNAs reveals extensive redundancy between SMG6- and SMG7-mediated degradation pathways.

Besides degrading aberrant mRNAs that harbor a premature translation termination codon (PTC), nonsense-mediated mRNA decay (NMD) also targets many seemingly "normal" mRNAs that encode for full-length proteins. To identify a bona fide set of such endogenous NMD targets in human cells, we applied a meta-analysis approach in which we combined transcriptome profiling of knockdowns and rescues of the three NMD factors UPF1, SMG6, and SMG7. We provide evidence that this combinatorial approach identifies NMD-targeted transcripts more reliably than previous attempts that focused on inactivation of single NMD factors. Our data revealed that SMG6 and SMG7 act on essentially the same transcripts, indicating extensive redundancy between the endo- and exonucleolytic decay routes. Besides mRNAs, we also identified as NMD targets many long noncoding RNAs as well as miRNA and snoRNA host genes. The NMD target feature with the most predictive value is an intron in the 3' UTR, followed by the presence of upstream open reading frames (uORFs) and long 3' UTRs. Furthermore, the 3' UTRs of NMD-targeted transcripts tend to have an increased GC content and to be phylogenetically less conserved when compared to 3' UTRs of NMD insensitive transcripts.

Artificial Lysosomal Platform to Study Nanoparticle Long-term Stability.

Nanoparticles (NPs) possess unique properties useful for designing specific functionalities for biomedi- cal applications. A prerequisite of a safe-by-design and effective use in any biomedical application is to study NP-cell interactions to gain a better understanding of cellular consequences upon exposure. Cellular uptake of NPs results mainly in the localization of NPs in the complex environment of lysosomes, a compartment which can be mimicked by artificial lysosomal fluid. In this work we showed the applicability of lysosomal fluid as a platform for a fast assessment of gold, iron oxide and silica NP stability over 24 h in a relevant biological fluid, by using multiple analytical methods.

Biodistribution of single and aggregated gold nanoparticles exposed to the human lung epithelial tissue barrier at the air-liquid interface.

BACKGROUND: The lung represents the primary entry route for airborne particles into the human body. Most studies addressed possible adverse effects using single (nano)particles, but aerosolic nanoparticles (NPs) tend to aggregate and form structures of several hundreds nm in diameter, changing the physico-chemical properties and interaction with cells. Our aim was to investigate how aggregation might affect the biodistribution; cellular uptake and translocation over time of aerosolized NPs at the air-blood barrier interface using a multicellular lung system. RESULTS: Model gold nanoparticles (AuNPs) were engineered and well characterized to compare single NPs with aggregated NPs with hydrodynamic diameter of 32 and 106 nm, respectively. Exposures were performed by aerosolization of the particles onto the air-liquid interface of a three dimensional (3D) lung model. Particle deposition, cellular uptake and translocation kinetics of single and aggregated AuNPs were determined for various concentrations, (30, 60, 150 and 300 ng/cm2) and time points (4, 24 and 48 h) using transmission electron microscopy and inductively coupled plasma optical emission spectroscopy. No apparent harmful effect for single and aggregated AuNPs was observed by lactate dehydrogenase assay, nor pro-inflammation response by tumor necrosis factor α assessment. The cell layer integrity was also not impaired. The bio-distribution revealed that majority of the AuNPs, single or aggregated, were inside the cells, and only a minor fraction, less than 5%, was found on the basolateral side. No significant difference was observed in the translocation rate. However, aggregated AuNPs showed a significantly faster cellular uptake than single AuNPs at the first time point, i.e. 4 h. CONCLUSIONS: Our studies revealed that aggregated AuNPs showed significantly faster cellular uptake than single AuNPs at the first time point, i.e. 4 h, but the uptake rate was similar at later time points. In addition, aggregation did not affect translocation rate across the lung barrier model since similar translocation rates were observed for single as well as aggregated AuNPs.

Rapid and sensitive quantification of cell-associated multi-walled carbon nanotubes.

Evaluating nanomaterial uptake and association by cells is relevant for in vitro studies related to safe-by-design approaches, nanomedicine or applications in photothermal therapy. However, standard analytical techniques are time-consuming, involve complex sample preparation or include labelling of the investigated sample system with e.g. fluorescent dyes. Here, we explore lock-in thermography to analyse and compare the association trends of epithelial cells, mesothelial cells, and macrophages exposed to gold nanoparticles and multi-walled carbon nanotubes over 24 h. The presence of nanomaterials in the cells was confirmed by dark field and transmission electron microscopy. The results obtained by lock-in thermography for gold nanoparticles were validated with inductively coupled plasma optical emission spectrometry; with data collected showing a good agreement between both techniques. Furthermore, we demonstrate the detection and quantification of carbon nanotube-cell association in a straightforward, non-destructive, and non-intrusive manner without the need to label the carbon nanotubes. Our results display the first approach in utilizing thermography to assess the carbon nanotube amount in cellular environments.

Reduction of Nanoparticle Load in Cells by Mitosis but Not Exocytosis.

The long-term fate of biomedically relevant nanoparticles (NPs) at the single cell level after uptake is not fully understood yet. We report that lysosomal exocytosis of NPs is not a mechanism to reduce the particle load. Biopersistent NPs such as nonporous silica and gold remain in cells for a prolonged time. The only reduction of the intracellular NP number is observed via cell division, e.g., mitosis. Additionally, NP distribution after cell division is observed to be asymmetrical, likely due to the inhomogeneous location and distribution of the NP-loaded intracellular vesicles in the mother cells. These findings are important for biomedical and hazard studies as the NP load per cell can vary significantly. Furthermore, we highlight the possibility of biopersistent NP accumulation over time within the mononuclear phagocyte system.

Revealing the Role of Epithelial Mechanics and Macrophage Clearance during Pulmonary Epithelial Injury Recovery in the Presence of Carbon Nanotubes.

Wound healing assays are extensively used to study tissue repair mechanisms; they are typically performed by means of physical (i.e., mechanical, electrical, or optical) detachment of the cells in order to create an open space in which live cells can lodge. Herein, an advanced system based on extensive photobleaching-induced apoptosis; providing a powerful tool to understand the repair response of lung epithelial tissue, consisting of a small injury area where apoptotic cells are still intact, is developed. Notably, the importance of epithelial mechanics and the presence of macrophages during the repair can be understood. The findings reveal that individual epithelial cells are able to clear the apoptotic cells by applying a pushing force, whilst macrophages actively phagocytose the dead cells to create an empty space. It is further shown that this repair mechanism is hampered when carbon nanotubes (CNTs) are introduced: formation of aberrant (i.e., thickening) F-actins, maturation of focal adhesion, and increase in traction force leading to retardation in cell migration are observed. The results provide a mechanistic view of how CNTs can interfere with lung repair.

Biodistribution, Clearance, and Long-Term Fate of Clinically Relevant Nanomaterials.

Realization of the immense potential of nanomaterials for biomedical applications will require a thorough understanding of how they interact with cells, tissues, and organs. There is evidence that, depending on their physicochemical properties and subsequent interactions, nanomaterials are indeed taken up by cells. However, the subsequent release and/or intracellular degradation of the materials, transfer to other cells, and/or translocation across tissue barriers are still poorly understood. The involvement of these cellular clearance mechanisms strongly influences the long-term fate of used nanomaterials, especially if one also considers repeated exposure. Several nanomaterials, such as liposomes and iron oxide, gold, or silica nanoparticles, are already approved by the American Food and Drug Administration for clinical trials; however, there is still a huge gap of knowledge concerning their fate in the body. Herein, clinically relevant nanomaterials, their possible modes of exposure, as well as the biological barriers they must overcome to be effective are reviewed. Furthermore, the biodistribution and kinetics of nanomaterials and their modes of clearance are discussed, knowledge of the long-term fates of a selection of nanomaterials is summarized, and the critical points that must be considered for future research are addressed.

Evaluation of cAMS for 14C microtracer ADME studies: opportunities to change the current drug development paradigm.

AIM: Although regulatory guidances require human metabolism information of drug candidates early in the development process, the human mass balance study (or hADME study), is performed relatively late. hADME studies typically involve the administration of a 14C-radiolabelled drug where biological samples are measured by conventional scintillation counting analysis. Another approach is the administration of therapeutic doses containing a 14C-microtracer followed by accelerator mass spectrometry (AMS) analysis, enabling hADME studies completion much earlier. Consequently, there is an opportunity to change the current drug development paradigm. MATERIALS & METHODS: To evaluate the applicability of the MICADAS-cAMS method, we successfully performed: the validation of MICADAS-cAMS for radioactivity quantification in biomatrices and, a rat ADME study, where the conventional methodology was assessed against a microtracer MICADAS-cAMS approach. RESULTS & DISCUSSION: Combustion AMS (cAMS) technology is applicable to microtracer studies. A favorable opinion from EMA to complete the hADME in a Phase I setting was received, opening the possibilities to change drug development.