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Gene expression profiles of precursor cells identify compounds that reduce NRP1 surface expression in macrophages: Implication for drug repositioning for COVID-19

Coronavirus disease 2019 (COVID-19) is transitioning from a pandemic to an endemic phase through recurring mutations. Initial efforts focused on developing strategies to mitigate infection of lung epithelial cells which are the primary targets of the SARS-CoV-2 virus using the affinity of the spike protein to human ACE2 receptor. SARS-CoV-2, however, infects additional cell types present in the lung such as macrophages through the alternate entry receptor Neuropilin 1 (NRP1). Developing novel therapeutic strategies to prevent SARS-CoV-2 infection of cells crucial for immunosurveillance could thus be integral to treat post-acute sequelae of COVID-19 (PASC). Since traditional drug development process takes a long time, it is imperative to establish new strategies that can be rapidly deployed to combat the dynamic nature of COVID-19 evolution and to contribute to prevention of future pandemics. We obtained the gene expression profiles of THP-1 monocytes from L1000-based Connectivity Map using CLUE, cloud- based software platform for the analysis of perturbational datasets to identify compounds that could reduce the expression level of NRP1. Out of 33,590 compounds, we analyzed the profiles of 45 compounds for their ability to reduce NRP1 expression. We selected the top five small molecule inhibitors predicted to decrease the expression of NRP1 for validation studies. All five selected compounds showed low cytotoxicity at tested doses and their ability to reduce NRP1 surface expression was evaluated in THP-1 monocytes, THP-1-derived macrophage like cells and human peripheral blood mononuclear cell (PBMC)-derived primary macrophages. Five compounds with the largest predicted reduction of NRP1 expression decreased macrophage NRP1 surface expression measured using flow cytometry and fluorescent microscopy assays in both cell line and primary macrophages. Using our computational approach, we identified 45 compounds that could potentially decrease NRP1 surface expression in macrophages based on their effect on THP-1 monocytes. Validation studies showed that such an approach can help to identify compounds for drug repositioning in target cells that are absent in the L1000 database. Our proposed approach can be applicable for the rapid compound exploration to combat novel cell types that SARS-CoV-2 targets for infection and could provide molecular bases for the development of new drugs.

Obesity and age are transmission risk factors for SARS-CoV-2 infection among exposed individuals

The coronavirus disease (COVID-19) pandemic has occurred in Massachusetts in multiple waves led by a series of emerging variants. While the evidence has linked obesity with severe symptoms of COVID-19, the effect of obesity on susceptibility to SARS-CoV-2 infection remains unclear. Identification of intrinsic factors, which increase the likelihood of exposed individuals succumbing to productive SARS-CoV-2 infection could help plan mitigation efforts to curb the illness. We aim to investigate whether obese individuals have a higher susceptibility to developing productive SARS-CoV-2 infection given comparable exposure to nonobese individuals. This case-control study leveraged data from the Mass General Brigham's (MGB) electronic medical records (EMR), containing 687,813 patients, to determine whether obesity at any age increases the proportion of infections. We used PCR results of 72,613 subjects who tested positive to SARS-CoV-2 or declared exposure to the virus independently of the result of the test. For this study, we defined susceptibility as the likelihood of testing positive upon suspected exposure. We demonstrate evidence that SARS-CoV-2 exposed obese individuals were more prone to become COVID positive than nonobese individuals [adjusted odds ratio = 1.34 (95% CI: 1.29-1.39)]. Temporal analysis showed significantly increased susceptibility in obese individuals across the duration of the pandemic in Massachusetts. Obese exposed individuals are at a higher risk of getting infected with SARS-CoV-2. This indicates that obesity is not only a risk factor for worsened outcomes but also increases the risk for infection upon exposure. Identifying such populations early will be crucial for curbing the spread of this infectious disease.

Extracellular vesicles produced by HIV-1 Nef-expressing cells induce myelin impairment and oligodendrocyte damage in the mouse central nervous system

HIV-associated neurocognitive disorders (HAND) are a spectrum of cognitive impairments that continue to affect approximately half of all HIV-positive individuals despite effective viral suppression through antiretroviral therapy (ART). White matter pathologies have persisted in the ART era, and the degree of white matter damage correlates with the degree of neurocognitive impairment in patients with HAND. The HIV protein Nef has been implicated in HAND pathogenesis, but its effect on white matter damage has not been well characterized. Here, utilizing in vivo, ex vivo, and in vitro methods, we demonstrate that Nef-containing extracellular vesicles (Nef EVs) disrupt myelin sheaths and inflict damage upon oligodendrocytes within the murine central nervous system. Intracranial injection of Nef EVs leads to reduced myelin basic protein (MBP) staining and a decreased number of CC1 + oligodendrocytes in the corpus callosum. Moreover, cerebellar slice cultures treated with Nef EVs exhibit diminished MBP expression and increased presence of unmyelinated axons. Primary mixed brain cultures and enriched oligodendrocyte precursor cell cultures exposed to Nef EVs display a decreased number of O4 + cells, indicative of oligodendrocyte impairment. These findings underscore the potential contribution of Nef EV-mediated damage to oligodendrocytes and myelin maintenance in the pathogenesis of HAND.

In silico Drug Screening Approach Using L1000-Based Connectivity Map and Its Application to COVID-19

Conventional drug screening methods search for a limited number of small molecules that directly interact with the target protein. This process can be slow, cumbersome and has driven the need for developing new drug screening approaches to counter rapidly emerging diseases such as COVID-19. We propose a pipeline for drug repurposing combining in silico drug candidate identification followed by in vitro characterization of these candidates. We first identified a gene target of interest, the entry receptor for the SARS-CoV-2 virus, angiotensin converting enzyme 2 (ACE2). Next, we employed a gene expression profile database, L1000-based Connectivity Map to query gene expression patterns in lung epithelial cells, which act as the primary site of SARS-CoV-2 infection. Using gene expression profiles from 5 different lung epithelial cell lines, we computationally identified 17 small molecules that were predicted to decrease ACE2 expression. We further performed a streamlined validation in the normal human epithelial cell line BEAS-2B to demonstrate that these compounds can indeed decrease ACE2 surface expression and to profile cell health and viability upon drug treatment. This proposed pipeline combining in silico drug compound identification and in vitro expression and viability characterization in relevant cell types can aid in the repurposing of FDA-approved drugs to combat rapidly emerging diseases.