ABSTRACT
Immune cells respond to environmental cues by way of receptors that trigger intracellular signalling cascades. These signalling cascades often involve transient protein-protein interactions. Detailed understanding of how and where in the cell intracellular proteins interact is required to understand how immune cells can be controlled and manipulated therapeutically. The function of numerous signalling proteins have been elucidated using traditional wet-lab methods. But there are many receptors for which the exact function and role remain uncertain. The expansion of large, high quality scRNA-seq databases following the Covid-19 pandemic have increased the applicability of data mining to answer outstanding questions in immunology. T-cell specific adaptor (TSAd), encoded by the SH2D2A gene, is an adaptor enriched in T and NK cells. Several interactors of TSAd, including the tyrosine kinases Lck and Itk, have been identified. However, what roles these interactions play in T and NK cell function remains unclear. To pick apart the TSAd interactome we have delved into available scRNA-seq datasets to determine genes and cell surface molecules that are concomitantly expressed with TSAd, making use of paired healthy and diseased samples to give a multi-faceted picture of the TSAd interactome. New interactors and the signals that control these interactions will be verified in genetically modified T or NK cells using classic wet-lab techniques such as pulldowns, as well as newer techniques such as the proximity ligation assay (PLA), with pilot work carried out on the established TSAd and Lck pair as a proof-of- concept.
ABSTRACT
Drug repositioning may be a promising way to find potential therapies against coronavirus disease 2019. Although chloroquine and hydroxychloroquine showed controversial results against the coronavirus disease 2019 disease, the potential common and diverging mechanisms of action are not reported and need to be dissected for better understanding them. An integrated strategy was proposed to systematically decipher the common and diverging aspects of mechanism of chloroquine and hydroxychloroquine against coronavirus disease 2019-disease network based on network pharmacology and in silico molecular docking. Potential targets of the two drugs and coronavirus disease 2019 related genes were collected from online public databases. Target function enrichment analysis, tissue enrichment maps and molecular docking analysis were carried out to facilitate the systematic understanding of common and diverging mechanisms of the two drugs. Our results showed that 51 chloroquine targets and 47 hydroxychloroquine targets were associated with coronavirus disease 2019. The core targets include tumor necrosis factor, glyceraldehyde 3-phosphate dehydrogenase, lymphocyte-specific protein-tyrosine kinase, beta-2 microglobulin, nuclear receptor coactivator 1, peroxisome proliferator-activated receptor gamma and glutathione disulfide reductase. Both chloroquine and hydroxychloroquine had good binding affinity towards tumor necrosis factor (affinity=-8.6 and -8.4 kcal/mol, respectively) and glyceraldehyde 3-phosphate dehydrogenase (-7.5 and -7.5 kcal/mol). Chloroquine and hydroxychloroquine both had good affinity with angiotensin-converting enzyme 2, 3-chymotrypsin-like protease and transmembrane serine protease 2. However, hydroxychloroquine manifested better binding affinity with the three proteins comparing with that of chloroquine. Chloroquine and hydroxychloroquine could have potential to inhibit over-activated immunity and inflammation. The potential tissue-specific regulation of the two drugs against severe acute respiratory syndrome coronavirus 2 infection may related with the lung, liver, brain, placenta, kidney, blood, eye, etc. In conclusion, our data systematically demonstrated chloroquine and hydroxychloroquine may have potential regulatory effects on coronavirus disease 2019 disease network, which may affect multiple organs, protein targets and pathways. Routine measurements of the chloroquine and hydroxychloroquine blood concentrations and tailored therapy regimen may be essential. But, further rigorous and high quality randomized controlled clinical trials are warranted to validate the antiviral effects of chloroquine and hydroxychloroquine against severe acute respiratory syndrome coronavirus 2. Our proposed strategy could facilitate the drug repurposing efforts for coronavirus disease 2019 treatment.