Transcriptomic Profiling of SARS-CoV-2 Infected Lung Endothelial Cells

Abstract Background: Cardiovascular sequelae of severe acute respiratory syndrome (SARS) coronavirus-2 (CoV-2) disease 2019 (COVID-19) contribute to the complications of the disease. One potential complication is lung endothelial dysfunction, but the exact cause remains unknown. We performed in-depth bulk transcriptomic analysis of human lung microvascular endothelial cells (HLMVECs) and pulmonary artery endothelial cells (PAECs) following in vitro SARS-CoV-2 infection as surrogates to compartment-specific transcriptome changes. Methods: HLMVECs and PAECs were infected with a multiplicity of infection (MOI) of 2 of SARS-CoV-2. After 6h, the cells were removed for RNA isolation, followed by bulk RNA sequencing (RNA-seq), read trimming and alignment to the human genome, and analysis of differentially expressed genes (DEGs). Ingenuity pathway analysis was conducted on DEGs. Infection was verified using quantitative real-time PCR (qRT-PCR) of SARS-CoV-2 Nucleocapsid (N), envelope (E), and spike (S) gene mRNAs prior to sequencing. Results: HLMVECs and PAECs showed amplification of SARS-CoV-2 N, E, and S protein mRNA following infection. HLMVECs had 1097 DEGs, with 576 downregulated DEGs and 521 upregulated DEGs. Main gene ontology (GO) cell functions that were affected in SARS-CoV-2 infected HLMVECs belonged to the categories “cell cycle, survival, and DNA repair”, “Cell movement and trafficking” and “Development”. Surprisingly, immune function was only represented in a fraction of the genes. In a detailed analysis of pathway activation, we discovered that many pathways affecting stem cell signaling, cell death, and immune signaling were predicted to be inhibited. Few pathways were predicted to be activated, including Coagulation System and PTEN Signaling. In contrast, PAECs exhibited 3813 DEGs, with 1756 downregulated and 2057 upregulated DEGs. Here, the main GO cell functions were similar to HLMVECs. Also, similar to HLMVECs, most identified pathways were predicted to be inhibited. However, the clustering of the pathways was different from HLMVECs and focused on mitochondrial function, cancer cell signaling, and endocrine signaling. Pathways with predicted activation included EIF2 Signaling, oxidative phosphorylation, and RHOA Signaling. Conclusion: Lung ECs exhibit fundamental transcriptomic changes in response to SARS-CoV-2 infection, demonstrating a predominant pattern of predicted inhibition. There are distinct differences between microvascular and pulmonary artery ECs that could explain functional differences. Further verification in vivo is needed to determine the translational value of our findings.