Differential Gene Expression of SARS-CoV-2 positive Bronchoalveolar Lavages: A Case Series

Transcriptomic data on bronchoalveolar lavage (BAL) from COVID-19 patients are currently scarce. This case series seeks to characterize the intraalveolar immunopathology of COVID-19. BALs were performed on 14 patients (5 COVID-19, of which 3 mild and 2 largely asymptomatic, 9 controls). Controls included asthma (n=1), unremarkable BALs (n=3), infections with respiratory syncytial virus (n=1), influenza B (n=1), and infections with other coronaviruses (n=3). SARS-CoV-2 RNA load was measured by quantitative nucleic acid testing (QNAT), while the detection of other pathogens was performed by immunofluorescence or multiplex NAT. Gene expression profiling was subsequently performed, showing 71 significantly downregulated and 5 upregulated transcripts in SARS-CoV-2-positive lavages versus controls. Downregulated transcripts included genes involved in macrophage development, polarization and crosstalk (LGALS3, MARCO, ERG2, BTK, RAC1, CD83), and genes involved in chemokine signaling and immunometabolism (NUPR1, CEBPB, CEBPA, PECAM1, CCL18, PPARG, ALOX5, ALOX5AP). Upregulated transcripts featured genes involved in NK-T cell signaling (GZMA, GZMH, GNLY, PRF1, CD3G). Patients with mild COVID-19 showed a significant upregulation of genes involved in blood mononuclear cell/leukocyte function (G0S2, ANXA6, FCGR2B, ADORA3), coagulation (VWF), interferon response (IFRD1, IL12RB2) and a zinc metalloprotease elevated in asthma (CPA3) compared to asymptomatic cases. In-silico comparison of the 5 COVID-19 BAL cases to a published cohort of lethal COVID-19 showed a significant upregulation of "antigen processing and presentation" and "lysosome" pathways in lethal cases. These data underscore the heterogeneity of immune response in COVID-19. Further studies with a larger dataset are required to gain a better understanding of the hallmarks of SARS-CoV-2 immunological response.