Imprinting and clonality of human NK cell memory

Introduction

The pool of innate immune effector cells is wired to rapidly respond to pathogens, whereas only few specificities within the naïve adaptive repertoire expand clonally, undergo epigenetic remodelling and differentiate into effector and memory cells. However, innate cells can differentiate upon pathogen encounter and remember past experiences as well, thereby challenging this strict dichotomy.

Background

In particular, us and others have shown that human memory Natural Killer (NK) cells with global epigenetic remodelling can be generated in response to specific signals during cytomegalovirus (CMV) infection. We have recently identified two major types of open chromatin domains in human memory NK (mNK) cells ex vivo:

1. A shared signature featured by all mNK cells across CMV-seropositive donors (“public memory”).
2. A diverse set of unique open chromatin regions associated with the drastic expansions of individual and stable NK cell clones (“private memory”).

Based on this unexpected finding, we hypothesise that the shared and the unique clonal memory might provide mNK cells with increased fitness and high effector potential, but also enhance the risk of oncogenic mutations.

Project Goals

The ultimate goal of this project is to identify the signals and molecular mechanisms driving acquisition, selection and maintenance of human NK cell public and private clonal memory.

Methodology

To this end, we will combine:

• Multiomic single cell assays
• Lineage tracing of human NK cells from healthy donors and patients ex vivo, or under various stimuli in vitro
• Genome-wide CRISPR perturbation studies to directly link ex vivo features with functional readouts.

Expected Outcomes

Success of this project will not only lead to new insights into the key networks promoting persistence and effector functions of mNK cells, but also reveal promising novel targets for cellular anti-tumour therapies.