Bulk Transcriptomics

"To elucidate the protective mechanism of an ADCC mAb against SARS-CoV-2 infection, we employed transcriptome analysis on K18-hACE2 transgenic mice with or without 5SB12 mAb pretreatment and SARS-CoV-2 challenge. There were four treatment groups, with two biological replicates from two different mice per group, indicated by Ab/Virus symbols (−/−, +/−, −/+, and +/+). After 5 days post-infection, lung tissues were harvested and the FFPE blocks were sectioned for both bulk RNA-seq and 10x Genomics Visium spatial transcriptomics sequencing. Our bulk RNA-seq libraries yielded an average of 65 million reads, while the spatial transcriptomics libraries yielded an average of 97 million reads (UMIs) per library. The sequencing quality of both sequencing types showed a mean quality score of >32. For bulk RNA-seq, approximately 95% of reads were mapped to the mouse reference genome, except in the virus-infected samples (−/+), where only 86.92% and 82.84% of reads mapped to the genome because a large portion belonged to SARS-CoV-2. Expression profiles between the two batches showed a high correlation across all treatment groups (Pearson’s correlation coefficient, r > 0.95). The number of detected SARS-CoV-2 transcripts was consistently lower in samples pretreated with 5SB12 mAb (+/+) than in those without mAb pretreatment (−/+). Principal component analysis showed that uninfected samples clustered together regardless of antibody pretreatment, whereas virus-infected samples without antibody pretreatment were positioned far from all other samples. Differential gene expression analysis identified no differentially expressed genes between −/− and +/− uninfected samples, suggesting that mAb pretreatment had minimal to no impact on the lung transcriptomics profile. In contrast, 936, 1074, and 539 differentially expressed genes were identified when comparing the −/+ infected samples with −/−, +/−, and +/+ samples, respectively. These findings indicate that 5SB12 mAb pretreatment does not alter the baseline lung transcriptome profile and effectively preserves a profile similar to that of uninfected controls after SARS-CoV-2 infection."