Comparative Transcriptomic and Molecular Pathway Analyses of HL-CZ Human Pro-Monocytic Cells Expressing SARS-CoV-2 Spike S1, S2, NP, NSP15 and NSP16 Genes

Abstract

The ongoing COVID-19 pandemic is a clear and present threat to global public health. Research into how the causative SARS-CoV-2 virus together with its individual constituent genes and proteins interact with target host cells can facilitate the development of improved strategies to manage the acute and long-term complications of COVID-19. In this study, to better understand the biological roles of critical SARS-CoV-2 proteins, we determined and compared the host transcriptomic responses of the HL-CZ human pro-monocytic cell line upon transfection with key viral genes encoding the spike S1 subunit, S2 subunit, nucleocapsid protein (NP), NSP15 (endoribonuclease), and NSP16 (2′-O-ribose-methyltransferase). RNA sequencing followed by gene set enrichment analysis and other bioinformatics tools revealed that host genes associated with topologically incorrect protein, virus receptor activity, heat shock protein binding, endoplasmic reticulum stress, antigen processing and presentation were up-regulated in the presence of viral spike S1 expression. With spike S2 expression, pro-monocytic genes associated with the interferon-gamma-mediated signaling pathway, regulation of phosphatidylinositol 3-kinase activity, adipocytokine signaling pathway, and insulin signaling pathway were down-regulated, whereas those associated with cytokine-mediated signaling were up-regulated. The expression of NSP15 induced the up-regulation of genes associated with neutrophil degranulation, neutrophil-mediated immunity, oxidative phosphorylation, prion disease, and pathways of neurodegeneration. The expression of NSP16 resulted in the down-regulation of genes associated with S-adenosylmethionine-dependent methyltransferase activity. The expression of NP down-regulated genes associated with positive regulation of neurogenesis, nervous system development, and heart development. Taken together, the complex transcriptomic alterations arising from these viral-host gene interactions offer useful insights into host genes and their pathways that potentially contribute to SARS-CoV-2 pathogenesis.

SARS-CoV-2 Spike Protein and Mouse Coronavirus Inhibit Biofilm Formation by Streptococcus pneumoniae and Staphylococcus aureus

“…Importantly, the spike protein is the major target antigen of vaccines against COVID-19, as well as the main site for mutations in SARS-CoV-2 variants, including Omicron [ 29 , 30 ]. Spike expression in human pro-monocytic cells can also dysregulate expression of host genes associated with virus receptor activity, heat shock protein binding, endoplasmic reticulum stress, antigen processing, and presentation [ 31 ]. The heavily glycosylated trimeric spike protein consists of two subunits—the S1 subunit contains a receptor-binding domain (RBD) that binds to the host cell receptor (angiotensin-converting enzyme 2 or ACE2), while the S2 subunit mediates fusion between the viral and host cell membranes [ 32 ].…”

Potential Coronaviral Inhibitors of the Nucleocapsid Protein Identified In Silico and In Vitro from a Large Natural Product Library

“…The nucleocapsid protein plays a major role in SARS-CoV-2 infection. It interferes with the expression of the stress granule formation G3BP1/2 and RIGL1 receptor pathway genes [32,33], increases cytokine, and chemokine production [34], and interferes with many other pathways in the human body [35]. NP also interacts with the NLRP3 inflammasome in mice by boosting the assembly and activation.…”

Combination Treatment With Remdesivir and Ivermectin Exerts Highly Synergistic and Potent Antiviral Activity Against Murine Coronavirus Infection

“…Autopsy analyses of COVID-19 patients reveal the presence of SARS-CoV-2 viral particles and antigen within lymph node and splenic macrophages. Aberrant mononuclear phagocyte activation or macrophage activation syndrome may lead to the cytokine release syndrome or "cytokine storm" which culminates in excessive inflammation and coagulopathy associated with COVID-19 severity and mortality (Merad and Martin, 2020;Sharma et al, 2021b). SARS-CoV-2-infected macrophages thus contribute to viral spread, exaggerated inflammation, and activation-induced lymphocytic cell death (Park, 2020).…”