Next generation sequencing transcriptome analysis of patient-derived macrophages after SARS-CoV-2 mRNA vaccination

Innate immunity triggers responsible for viral control or hyperinflammation in COVID-19 are largely unknown. Recently we could show that the SARS-CoV-2 spike protein (S-protein) primes inflammasome formation and release of mature interleukin-1ß (IL-1ß) in macrophages derived from COVID-19 patients but not in macrophages from healthy SARS-CoV-2 naïve individuals (Theobald et al. EMBO Mol Med. 2021). Further analysis revealed that SARS-CoV-2 infection causes profound and long-lived reprogramming of macrophages resulting in augmented immunogenicity of the SARS-CoV-2 S-protein, a major vaccine antigen and potent driver of adaptive and innate immune signaling. In this project we want to focus on novel mRNA vaccines, which are exploiting S-protein driven immunogenicity for protection against SARS-CoV-2. Transcriptome analyses of macrophages might reveal differences in innate immune-associated pathways between vaccinated and unvaccinated individuals after prime-boost. Thus, our project could help to gain a better understanding of vaccine-induced immunity including underlying molecular mechanisms in the interaction of the innate and adaptive immune system after mRNA-based SARS-CoV-2 vaccination. Overall design: Macrophages of vaccinated (n = 6) and unvaccinated (n = 6) individuals were stimulated with SARS-CoV-2 spike protein (S-protein), lipopolysaccharide (LPS) or left unstimulated. All experiments were performed in technical triplicates. In total 36 samples are provided (3 conditions (unstimulated, LPS and S-protein) from 12 different individuals (6 vaccinated; 6 unvaccinated). LPS is a classical PAMP, known for its strong activation of inflammasome/inflammation-associated pathways and it's used in our experiments as control for activation of the inflammation-associated genes and pathways. Recombinant SARS-CoV-2 spike protein is used in our experiments to mimic reexposition with SARS-CoV-2 mRNA vaccine, which is based on the spike protein production by the host or SARS-CoV-2 infection. To get a deeper understanding of spike protein induced immunity we would like to analyze differences in gene expression of macrophages from vaccinated vs unvaccinated inidividuals exposed to the different stimuli (unstimulated, LPS, S-protein). Moreover we would like to compare differences within the two groups (vaccinated or unvaccinated) in response to LPS or S-protein.