# PROJECT 2: INNATE IMMUNITY

> **NIH NIH U19** · EMORY UNIVERSITY · 2024 · $396,354

## Abstract

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.

## Key facts

- **NIH application ID:** 10825212
- **Project number:** 2U19AI057266-21
- **Recipient organization:** EMORY UNIVERSITY
- **Principal Investigator:** Rafi Ahmed
- **Activity code:** U19 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $396,354
- **Award type:** 2
- **Project period:** 2003-09-01 → 2029-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10825212

## Citation

> US National Institutes of Health, RePORTER application 10825212, PROJECT 2: INNATE IMMUNITY (2U19AI057266-21). Retrieved via AI Analytics 2026-05-25 from https://api.ai-analytics.org/grant/nih/10825212. Licensed CC0.

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