Comparative in vitro transcriptomic analyses of COVID-19 candidate therapy hydroxychloroquine suggest limited immunomodulatory evidence of SARS-CoV-2 host response genes.

Michael Jay Corley; Christopher Sugai; Michael Schotsaert; Robert E. Schwartz; Lishomwa C Ndhlovu

The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.13.039263 doi: bioRxiv preprint from three male individuals infected with SARS-CoV-2 and three control individuals without SARS-CoV-2 infection obtained from China (Supplemental Table 1 ) [20] . We first sought to confirm the observed immunological changes observed during COVID-19 disease in peripheral blood by others [15, [21] [22] [23] [24] . We utilized the bulk transcriptome PBMC data and estimated the abundances of 22 immune cell types using the CIBERSORT analytical deconvolution tool [25] . Similar to other reports, we observed a drastic expansion of monocyte cells in peripheral blood of COVID-19 participants (75.3%, 46.4%, and 57.4%) compared to controls (19.8%, 5.6%, and 26.8%) using an estimation of member cell types in PBMC based on gene expression data ( Fig. 2a, Supplemental Figure 2) . Also, we saw that CD4 memory resting cells and NK cells resting drastically reduced in all three COVID-19 participants compared to controls (Fig. 2a, Supplemental Figure 2 ). differentially expressed genes related to COVID-19, we identified that only 5 genes overlapped between the gene set of HCQ-related transcriptional changes and COVID-19-related transcriptional changes in PBMC (Fig. 2b ). This accounted for only 0.24% of the host related COVID-19 transcriptional changes in PBMC, suggesting HCQ minimally restores/impacts COVID-19-related transcriptional immune changes. In the HCQ PBMC transcriptional dataset, we observed that the IL1R2, FN1, and A2M were significantly downregulated and LDLR and SCD gene were significantly upregulated (Fig.2c ). In the COVID-19 PBMC transcriptional dataset, we observed that the LDLR gene was significantly upregulated similar to the SARS-CoV-2 in vitro infection dataset for NHBE (Fig.2d) . Additionally, in the COVID-19 PBMC dataset, the IL1R2, FN1, and SCD genes were significantly upregulated compared to a significant downregulation of the A2M gene (Fig.2d) . These results should be taken with caution as studies are needed comparing PBMC cells from COVID-19 participants before and after HCQ treatment. Additionally, whether the directionally of transcriptional change in PBMC cells due to HCQ treatment or related to COVID-19 has any immunomodulatory effect leading to clinical benefits requires further study. This comparative analysis is limited and does not address whether HCQ has antiviral effects by reducing SARS-CoV-2 virus entry through impacting cell lipid metabolism pathways since author/funder. All rights reserved. No reuse allowed without permission.