Transcriptome Profile Alterations with Carbon Nanotubes, Quantum Dots, and Silver Nanoparticles: A Review.

Next-generation sequencing (NGS) technology has revolutionized sequence-based research. In recent years, high-throughput sequencing has become the method of choice in studying the toxicity of chemical agents through observing and measuring changes in transcript levels. Engineered nanomaterial (ENM)-toxicity has become a major field of research and has adopted microarray and newer RNA-Seq methods. Recently, nanotechnology has become a promising tool in the diagnosis and treatment of several diseases in humans. However, due to their high stability, they are likely capable of remaining in the body and environment for long periods of time. Their mechanisms of toxicity and long-lasting effects on our health is still poorly understood. This review explores the effects of three ENMs including carbon nanotubes (CNTs), quantum dots (QDs), and Ag nanoparticles (AgNPs) by cross examining publications on transcriptomic changes induced by these nanomaterials.

Comparing Transcriptome Profiles of Saccharomyces Cerevisiae Cells Exposed to Cadmium Selenide/Zinc Sulfide and Indium Phosphide/Zinc Sulfide.

The primary focus of our research was to obtain global gene expression data in baker's yeast exposed to sub-lethal doses of quantum dots (QDs), such as green-emitting CdSe/ZnS and InP/ZnS, to reveal novel insights on their unique mechanisms of toxicity. Despite their promising applications, their toxicity and long-lasting effects on the environment are not well understood. To assess toxicity, we conducted cell viability assays, ROS detection assays, and assessed their effects on the trafficking of Vps10-GFP toward the trans-Golgi network with confocal microscopy. Most notably, we used RNA-sequencing (RNA-seq) to obtain gene expression profiles and gene identities of differentially expressed genes (DEGs) in QD-treated yeast. We found CdSe/ZnS QDs significantly altered genes implicated in carboxylic acid, amino acid, nitrogen compounds, protein metabolic processes, transmembrane transport, cellular homeostasis, cell wall organization, translation, and ribosomal biogenesis. Additionally, we found InP/ZnS QDs to alter genes associated with oxidation-reduction, transmembrane transport, metal ion homeostasis, cellular component organization, translation, and protein and nitrogen compound metabolic processes. Interestingly, we observed an increase in reactive oxygen species (ROS) in CdSe/ZnS-treated cells and a decrease in ROS levels in InP/ZnS-treated cells. Nevertheless, we concluded that both QDs modestly contributed cytotoxic effects on the budding yeast.

Transcriptome Profile Alteration with Cadmium Selenide/Zinc Sulfide Quantum Dots in Saccharomyces cerevisiae.

Quantum Dots (QDs) are becoming more prevalent in products used in our daily lives, such as TVs and laptops, due to their unique and tunable optical properties. The possibility of using QDs as fluorescent probes in applications, such as medical imaging, has been a topic of interest for some time, but their potential toxicity and long-term effects on the environment are not well understood. In the present study, we investigated the effects of yellow CdSe/ZnS-QDs on Saccharomyces cerevisiae. We utilized growth assays, RNA-seq, reactive oxygen species (ROS) detection assays, and cell wall stability experiments to investigate the potential toxic effects of CdSe/ZnS-QDs. We found CdSe/ZnS-QDs had no negative effects on cell viability; however, cell wall-compromised cells showed more sensitivity in the presence of 10 µg/mL CdSe/ZnS-QDs compared to non-treated cells. In CdSe/ZnS-treated and non-treated cells, no significant change in superoxide was detected, but according to our transcriptomic analysis, thousands of genes in CdSe/ZnS-treated cells became differentially expressed. Four significantly differentiated genes found, including FAF1, SDA1, DAN1, and TIR1, were validated by consistent results with RT-qPCR assays. Our transcriptome analysis led us to conclude that exposure of CdSe/ZnS-QDs on yeast significantly affected genes implicated in multiple cellular processes.

Transcriptome profile with 20 nm silver nanoparticles in yeast.

Engineered nanomaterials are commercially used in everyday products including zinc sunscreens and water-resistant fabrics and surfaces. Therefore, understanding the effects of engineered nanomaterials on the environment is crucial for the responsible use of these technologies. We investigated the effects of 20 nm spherical citrate-coated silver nanoparticles (AgNPs) on the budding yeast Saccharomyces cerevisiae. Our growth assay showed that AgNPs have an inhibitory effect on yeast growth with concentrations above 5 µg/mL. Hundreds of genes in AgNP-treated cells were differentially expressed according to our transcriptome analysis based on RNAseq, including genes implicated in rRNA processing, ribosome biogenesis, cell wall formation, cell membrane integrity and mitochondrial functions. In particular, genes whose functions are associated with processing of small and large subunits of ribosomes were upregulated, while genes for cell wall/plasma membrane/mitochondrial integrity were downregulated. Consistently, our cell wall stability assay confirmed that cells with AgNPs are more susceptible to cell wall damage than non-treated cells. Levels of four significantly altered genes with AgNPs, including FAF1, SDA1, TIR1 and DAN1, were validated by reproducible results with RT-qPCR assays. Our transcriptome profile leads us to conclude that the exposure of cells to sublethal amounts of AgNPs affects many cellular processes negatively.