Integrative transcriptome analysis of SARS-CoV-2 human-infected cells combined with deep learning algorithms identifies two potential cellular targets for the treatment of coronavirus disease.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) quickly spread worldwide, leading coronavirus disease 2019 (COVID-19) to hit pandemic level less than 4 months after the first official cases. Hence, the search for drugs and vaccines that could prevent or treat infections by SARS-CoV-2 began, intending to reduce a possible collapse of health systems. After 2 years, efforts to find therapies to treat COVID-19 continue. However, there is still much to be understood about the virus' pathology. Tools such as transcriptomics have been used to understand the impact of SARS-CoV-2 on different cells isolated from various tissues, leaving datasets in the databases that integrate genes and differentially expressed pathways during SARS-CoV-2 infection. After retrieving transcriptome datasets from different human cells infected with SARS-CoV-2 available in the database, we performed an integrative analysis associated with deep learning algorithms to determine differentially expressed targets mainly after infection. The targets found represented a fructose transporter (GLUT5) and a component of proteasome 26s. These targets were then molecularly modeled, followed by molecular docking that identified potential inhibitors for both structures. Once the inhibition of structures that have the expression increased by the virus can represent a strategy for reducing the viral replication by selecting infected cells, associating these bioinformatics tools, therefore, can be helpful in the screening of molecules being tested for new uses, saving financial resources, time, and making a personalized screening for each infectious disease.

Integrative transcriptome analysis of human cells treated with silver nanoparticles reveals a distinct cellular response and the importance of inorganic elements detoxification pathways.

The field of Nanotechnology has taken a great leap in recent decades, with several products currently researched in the industrial sector and even available in the market bringing nanostructured components. The pharmaceutical industry has explored this type of structure as targeted drug delivery, especially against cancer. Integrative transcriptome analysis (ITA) is considered a promising technique for understanding biological events by analyzing several transcriptomes deposited in public databases. This research recovered seven transcriptomes' studies of human cells treated with silver nanoparticles without association or conjugation with any other substance or material for the performance of ITA. This analysis consists of a bipartite network for determining shared differentially expressed genes (DEGs) between different datasets from human cells treated with silver nanoparticles (AgNPs) at both early (4 or 6 h) and late treatment time (24 h). Most of the few upregulated DEGs shared by five or more datasets belong to biological pathways related to mineral absorption, suggesting that these processes were upregulated in AgNPs-treated cells. In addition, Ferroptosis, protein processing in the endoplasmic reticulum, and mitogen-activated protein kinase (MAPK) signaling pathway were also upregulated. Thus, the ITA of human cells treated with AgNPs indicates that the expression profile induced by these nanoparticles is specific to each cell type. However, they share inorganic compounds and oxidative stress responses genes, triggering apoptosis. This work reinforces the need for the biological characterization of cellular response to silver nanoparticles for application in humans, thus ensuring the safety and optimization of the desired results.

Nanoparticles as Vaccines to Prevent Arbovirus Infection: A Long Road Ahead.

Arthropod-borne viruses (arboviruses) are a significant public health problem worldwide. Vaccination is considered one of the most effective ways to control arbovirus diseases in the human population. Nanoparticles have been widely explored as new vaccine platforms. Although nanoparticles' potential to act as new vaccines against infectious diseases has been identified, nanotechnology's impact on developing new vaccines to prevent arboviruses is unclear. Thus, we used a comprehensive bibliographic survey to integrate data concerning the use of diverse nanoparticles as vaccines against medically important arboviruses. Our analysis showed that considerable research had been conducted to develop and evaluate nanovaccines against Chikungunya virus, Dengue virus, Zika virus, Japanese encephalitis virus, and West Nile virus. The main findings indicate that nanoparticles have great potential for use as a new vaccine system against arboviruses. Most of the studies showed an increase in neutralizing antibody production after mouse immunization. Nevertheless, even with significant advances in this field, further efforts are necessary to address the nanoparticles' potential to act as a vaccine against these arboviruses. To promote advances in the field, we proposed a roadmap to help researchers better characterize and evaluate nanovaccines against medically important arboviruses.