ABSTRACT Immunological memory is a fundamental feature of the adaptive immune system. However emerging evidence demonstrates that the innate immune system can also display a form of adaptive, memory-like behavior, a phenomenon termed “trained immunity.” Recently using single cell ATAC-seq we demonstrated that immunization of humans with the AS03-adjuvanted H5N1 pandemic influenza vaccine stimulates persistent epigenomic imprints in blood myeloid cells, that results in a heightened resistance to infection with heterologous viruses Zika and Dengue viruses, and reduced chromatin accessibility of loci targeted by the AP-1 transcription factors leading to reduced capacity to produce pro-inflammatory cytokines. These observations raise several key questions: 1) Do SARS-CoV-2 infection and vaccination stimulate functionally distinct long-term epigenetic innate reprogramming? 2) Is epigenetic imprinting of innate immunity “tunable,” by sequential infections or vaccinations? 3) What is the impact of SARS-CoV-2 vaccination or infection on epigenetic imprinting of innate immunity in tissues? 4) What are the mechanisms of innate memory induced by vaccination and their effects on protection against heterologous pathogens? These questions will be addressed in the following specific aims: Aim 1. Perform a longitudinal analysis of the evolution of the innate response following sequential rounds of SARS-CoV-2 infection or vaccination. We will perform a longitudinal analysis of the single cell transcriptional and epigenetic landscape of the innate immune system using banked PBMCs collected before, during and after infection from a COVID-19 cohort of healthcare workers and followed longitudinally from the beginning of the pandemic, through every infection and vaccination. Aim 2. Define the transcriptional and epigenetic landscape and function of myeloid cells in tissues. Most studies have only examined epigenetic imprinting of innate immunity in the blood, and the effects in tissues remain unclear. In sub-aim 2a we will assess the transcriptional and epigenomic landscape of myeloid-lineage cells in human mucosal and lymphoid tissues obtained from organ donors. In sub-aim 2b, we will use banked samples from completed studies in nonhuman primates to assess the transcriptional and epigenomic landscape of innate immune cells in various tissues and blood following SARS-CoV-2 infection or vaccination. Aim 3: To assess the mechanisms of innate memory induced by vaccination and their effects on protection against heterologous pathogens. In this aim we will use mice to explore the mechanisms underlying innate memory to vaccination, and its functional consequences on protection against heterologous infections.

We will use novel systems biological approaches to determine whether the evolutionarily ancient innate immune system has “immunological memory,” long thought to be a unique feature of the adaptive immune system. This will be explored in humans in the context of SARS-CoV-2 infection and vaccination.