COVID-19 outbreak is the biggest threat to human health in recent history. Currently, there are over 1.5 million related deaths and 75 million people infected around the world (as of 22/12/2020). The identification of virulence factors which determine disease susceptibility and severity in different cell types remains an essential challenge. The serine protease TMPRSS2 has been shown to be important for S protein priming and viral entry, however, little is known about its regulation. SPINT2 is a member of the family of Kunitz type serine protease inhibitors and has been shown to inhibit TMPRSS2 . Here, we explored the existence of a co-regulation between SPINT2 / TMPRSS2 and found a tightly regulated protease/inhibitor expression balance across tissues. We found that SPINT2 negatively correlates with SARS-CoV-2 expression in Calu-3 and Caco-2 cell lines and was down-regulated in secretory cells from COVID-19 patients. We validated our findings using Calu-3 cell lines and observed a strong increase in viral load after SPINT2 knockdown, while overexpression lead to a drastic reduction of the viral load. Additionally, we evaluated the expression of SPINT2 in datasets from comorbid diseases using bulk and scRNA-seq data. We observed its down-regulation in colon, kidney and liver tumors as well as in alpha pancreatic islets cells from diabetes Type 2 patients, which could have implications for the observed comorbidities in COVID-19 patients suffering from chronic diseases. Author summary Since early 2020, the world is facing a unique pandemic situation triggered by the appearance of a new coronavirus, Sars-CoV-2. While it shares similarities with previous coronaviruses, it shows some unique features, which requires in-depth investigations to understand its mechanisms of action, in particular the type of cells which can be infected, and the mechanism of cellular entry. We describe a new important actor which plays a decisive role in the entry of the virus into the cell. The serine protease inhibitor SPINT2 inhibits the well described serine protease TMPRSS2 , and we show that inhibiting or overexpressing this gene leads to an increase, respectively a strong decrease of the number of infected cells. Intriguingly, this gene has been described in the context of diseases which are known to be comorbid with COVD19, for example Type 2 diabetes and several malignancies. Using published datasets, we show that in these comorbid diseases, SPINT2 is downregulated, which might lead to an increase of the infectivity of cells in disease-tissues such as endocrine cells of diabetic patients or cells from tumor tissues.
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