Open Research Projects, Research

Role of persistent herpesvirus in shaping innate immune clonality

Prinicipal Investigator

Scientific interest within the context of the graduate college:

The innate immune system matures early on along with tissue development. In particular, innate lymphoid cells (ILCs, including Natural Killer (NK) cells, already colonize tissues during fetal life and acquire their effector functions already pre-natally. However, exposure to different environmental signals, including microbial infection, can still remodel ILCs and leave permanent epigenetic marks. Our group focuses on delineating transcriptionally and epigenetically the immune functional programs pre-wired during development as well as those emerged and imprinted after exposure to environmental stimuli, in particular persistent virus, thereby setting the threshold of our immune fitness and tolerance to tissue damage. Our aim is to understand the key homeostatic checkpoints, which, once altered, can initiate inflammatory circuits and lead to disease.

Project description:

Aim 1: Analysis of ex vivo dynamics of NK cell clonality and epigenetic remodeling in response to HCMV. In this part of the project, we aim to understand how NK cell clonal expansions are generated and maintained. To this aim, we will perform the following experiments:
A) Lineage tracing over time of human NKG2C+ and NKG2C NK cells derived from peripheral blood of HCMV+ and HCMV healthy individuals by performing scATACseq/scRNAseq and analysis of mitochondrial mutations (DOGMAseq).5
B) Lineage tracing over time of human NKG2C+ and NKG2C donor NK cells in patients undergoing hematopoietic stem cell transplantation and HCMV reactivation (established cooperation with Hematology Charité, Prof L. Büllinger). NK cells will be isolated from peripheral blood of patients between day 10 and day 30 after transplantation, during HCMV reactivation (typically around day 30), and at later time points (day 60-120). DOGMAseq will be performed as in 1A. Moreover, clinical and laboratory parameters along with sequencing of HCMV-relevant proteins will be assessed.

Aim 2: Analysis of in vitro dynamics of NK cell clonality and epigenetic remodeling in response to HCMV-derived signals. In this part of the project, we aim to understand the signals driving NK cell clonal expansion. To this aim, we will mimic NK cell clonal expansion in vitro by culturing human NKG2C+ “naive” NK cells derived from peripheral blood of HCMV healthy individuals in the presence of signals mimicking HCMV stimulation (NKG2C peptide ligands, CD2 costimulation, and pro-inflammatory cytokines). Proliferating NK cells will be sorted at different time points and DOGMA-seq will be performed.

Application details


  1. Luetke-Eversloh M, Hammer Q, Durek P, […], Chang HD, Dong J, RomagnaniC. Human cytomegalovirus drives epigenetic imprinting of the IFNG locus in NKG2Chi natural killer cells. PLoS Pathog. 2014; 10:e1004441. doi: 10.1371/journal.ppat.1004441.
  2. Hammer Q, Rückert T, Romagnani C. Natural killer cell specificity for viral infections. Nat Immunol. 2018; 19:800-808. doi: 10.1038/s41590-018-0163-6.
  3. Hammer Q, Rückert T, Borst EM, […], Mashreghi MF, Messerle M, Romagnani C. Peptide-specific recognition of human cytomegalovirus strains controls adaptive natural killer cells. Nat Immunol. 2018; 19:453-463. doi: 10.1038/s41590-018-0082-6.
  4. Ludwig LS, Lareau CA, Ulirsch JC, […], Buenrostro JD, Regev A, Sankaran VG. Lineage Tracing in Humans Enabled by Mitochondrial Mutations and Single-Cell Genomics. Cell. 2019; 176:1325-1339.e22. doi: 10.1016/j.cell.2019.01.022.
  5. Mimitou EP, Lareau CA, Chen KY, Sankaran VG, Regev A, Smibert P. Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells. Nat Biotechnol. 2021; 39:1246-1258. doi: 10.1038/s41587-021-00927-2.