Targeting CHI3L1 inhibits SARS-CoV-2 variants including Delta and Omicron

Coronavirus disease 2019 (COVID-19) is caused by infection with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), which has created a global pandemic with high morbidity and mortality. Early strains of SARS-CoV-2 were found to have low viral genetic diversity; however, recent genomic and epidemiological studies have found significant genetic heterogeneity in these viral strains.

To study: Host Chitinase 3-like-1 is a universal therapeutic target for delta, Omicron and other SARS-CoV-2 viral variants in COVID 19. Image Credit: Liro Lem/Shutterstock.com

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Many SARS-CoV-2 variants are now classified as variants of concern (VOC) due to genetic changes in their spike (S) and other proteins that result in increased transmissibility, reduced susceptibility to neutralizing antibodies or treatments, or the propensity to cause serious illness. Due to their exceptional and unparalleled transmissibility and ability to produce hard-hitting infections, the Delta and Omicron variants are of particular concern. The SARS-CoV-2 Delta variant, for example, accumulates in large quantities in host organs, leading to waves of deadly disease.

SARS-CoV-2 infection is caused by spike (S) protein binding to cell receptors for angiotensin-converting enzyme 2 (ACE2), which is then processed by protease from the protein S (SPP). A recent study found that chitinase 3-like-1 (CHI3L1) promotes ACE2 and SPPs. The researchers of this study recently published New Investigators, in which they determine whether therapies targeted at CHI3L1 are effective inhibitors of infection by the viral variant SC2.

In the current study, which is posted on the preprint server bioRxiv*, researchers show that anti-CHI3L1 CHI3L1 inhibitors and kasugamycin (KSM) reduce infection of epithelial cells by VOCs pseudovirus fragments that express Alpha, Beta, Gamma, Delta or Omicron S proteins. Anti-CHI3L1 and KSM have also been shown to inhibit infection of epithelial cells by these VOC pseudovirus fragments.

Study results

CHI3L1 is a potent promoter of epithelial production of ACE2 and SPP, as well as viral uptake of epithelial cells. The researchers in the present study investigated the uptake of COV pseudoviruses with ancestral and mutant S proteins by untreated and CHI3L1-treated Calu-3 cells to determine whether major variations in S impact these responses.

The results suggest that CHI3L1 was an effective enhancer of pseudovirus uptake along with the former G614 S protein. When S proteins of the Alpha, Beta, or Gamma variants were used, similar increases in pseudovirus uptake of Calu cells -3 were observed. In fact, when the ancestral mutations of the D614G and Alpha, Beta or Gamma S proteins are present, CHI3L1 increases the uptake of the SARS-CoV-2 pseudovirus when.

The effects of the anti-CHI3L1 monoclonal antibody “FRG” on the uptake of the pseudovirus by Calu-3 cells were evaluated by treating the cells with and without CHI3L1. Treatment of Calu-3 cells with rCHI3L1 increased pseudovirus uptake, which was inhibited by FRG, but not by IgG control, as shown with the ancestral G614 S protein mutation. Interestingly, FRG reduced pseudovirus uptake by Calu-3 cells, even when exogenous rCHI3L1 was not provided.

In tests using pseudoviruses with Alpha, Beta, Gamma, Delta, or Omicron S protein mutations, rCHI3L1 produced similar stimulatory effects. Importantly, FRG significantly reduced pseudovirus uptake with each of the S mutations in cells treated with and without rCHI3L1. These results demonstrate that monoclonal anti-CHI3L1 targeting exogenous and/or endogenous CHI3L1 effectively blocks uptake of pseudoviruses with ancestral mutations and all VOC proteins.

KSM, an aminoglycoside antibiotic, is a new small molecule with potent anti-chitinase 1 (CHIT1) properties. Since both CHIT1 and CHI3L1 are members of the 18-glycohydrolase family, the researchers wanted to determine whether KSM inhibits the activity of CHI3L1 in the same way as CHIT1. To this end, KSM treatment of Calu-3 cells inhibited CHI3L1-stimulated activation of extracellular receptor kinase (ERK) and protein kinase B AKT, indicating that KSM has potent anti-CHI3L1 activity.

The ability of KSM to alter the ability of SARS-CoV-2 Delta and Omicron variants to infect human epithelial cells was also tested. CHI3L1 has been shown to be an effective activator of pseudovirus uptake with Delta and Omicron S protein mutations.

This increase was stopped by KSM, but not by vehicle control. Even when exogenous CHI3L1 was not used, KSM reduced pseudovirus uptake by Calu-3 cells.

Immunocytochemical assays supported these findings, in which researchers demonstrated that CHI3L1 increased ACE2 accumulation and Delta pseudovirus infection in Calu-3 cells. FRG was also found to suppress the expression of Delta and Omicron pseudovirus infection before and after rCHI3L1 injection.

Taken together, these results show that KSM targeting exogenous or endogenous CHI3L1 effectively suppresses uptake of pseudoviruses with Alpha, Beta, Gamma, Delta, or Omicron S protein mutations.

Consequences

Current research adds to the knowledge of early-stage SARS-CoV-2 therapeutics by demonstrating that inhibition of ChI3L1 with FRG and/or Kasugamycin reduces infection caused by Alpha, Beta, Gamma, Delta and Omicron SARS-CoV- 2 variants. This suggests the intriguing prospect that FRG or Kasugamycin, alone or in combination with each other or with other SARS-CoV-2 monoclonal antibodies, could have potent antiviral effects and/or limit viral infection in people exposed to SARS-CoV-2.

The researchers also demonstrate that FRG and kasugamycin can reduce viral replication and therefore disease pathophysiology and severity by lowering viral load. Although these findings are promising, further research on the importance of CHI3L1 and its role in infections induced by SARS-CoV-2 variants is needed.

*Important Notice

bioRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be considered conclusive, guide clinical practice/health-related behaviors, or treated as established information.