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

Immune regulation and defenses against viral pathogens occur within in the lung. We sought to examine whether the differential gene expression signatures of HCQ in immune cells associated with a COVID-19related transcriptional profile in the lung. We analyzed a limited transcriptomic data from postmortem lung biopsies obtained from two male participants with COVID-19 over the age of 60 years and two uninfected agematched control male participants (Supplemental Table 1 ). The COVID-19 and uninfected control participants were confirmed to not have been on HCQ treatment. As expected, we also detected 108 viral SARS-CoV-2 reads in the bulk RNA-Seq lung dataset of one of the COVID-19 individuals and 7 viral SARS-CoV-2 reads in the second COVID-19 participant (Supplemental Figure 6) . These results are limited by the low sequencing depth and 3' bias but do offer an interesting means to confirm COVID-19 infection by RNA-seq screening in postmortem samples. Our comparative analysis of the both PBMC and macrophage HCQ-treated gene sets with the COVID-19 postmortem lung transcriptional dataset identified only 5 overlapping genes (Fig.5a) . This overlap included CCL18, FOS, MMP1, ITGB3, and AQP9 genes. Notably, our gene ontology analysis of the COVID-19 postmortem lung dataset showed the top GO Biological Process as negative regulation of viral genome replication, GO Molecular Function as chemokine activity, and GO Cellular Component as secretory granule lumen. Additionally, we used CIBERSORT [25] to examine the immune cell populations in COVID-19 lung compared to uninfected lung (Supplemental Figure 7) . This deconvolution analysis showed some interesting initial differences of interest for further study. First, the relative fraction of CD4 memory resting T cells was 15% and 19% in the uninfected lungs compared to only 3% and 4% for the COVID-19 lung. Second, author/funder. All rights reserved. No reuse allowed without permission.