Studying Long-Term Memory of NK Cells through Clonal Expansion and Epigenetics
Summary
The researchers studied the ability of the innate immune system to adapt to specific pathogens by examining the memory of natural killer (NK) cells in response to human cytomegalovirus (HCMV) infection. Using single cell multiomic maps of ex vivo NK cells and somatic mitochondrial DNA mutations as markers, they found significant clonal expansion of adaptive NK cells in individuals infected with HCMV. The clonotypes of these cells were characterized by an inflammatory memory signature enriched with AP1 motifs and private, clonotype-specific accessible chromatin regions. The researchers also observed that NK cell clones retained unique epigenetic states over time, indicating that the inheritance of chromatin accessibility plays a role in the formation of the epigenetic memory repertoire. This study identified clonal expansion and persistence in the human innate immune system, suggesting that these mechanisms evolved independently of antigen-receptor diversity.
Research Criteria
The scientists developed a single cell multiomic map of human natural killer (NK) cells from persons infected or uninfected with human cytomegalovirus (HCMV). They combined measurements of gene expression and chromatin accessibility with mitochondrial DNA-based lineage tracking (mtDNA). They discovered a considerable clonal expansion of adaptive NK cells with an inflammatory memory signature and private, clonotype-specific accessible chromatin regions, demonstrating that a population of human innate immune cells survive in a memory state via clonal expansion.
Fig.1 NKG2C+ and NKG2C- NK cells were isolated from four to five HCMV+ individuals and two HCMV-healthy blood donors. (Rückert, 2022)
Sample Type
Primary NK cells were isolated from freshly drawn peripheral blood of healthy people or buffy coats.
Fig.2 Sorting strategy for one representative HCMV- and HCMV+ donor respectively. (Rückert, 2022)
Result—Mapping NK Cell Subsets onto Transcriptional and Epigenetic Landscape
Single-cell assay of transposase-accessible chromatin (ATAC) with select antigen profiling by sequencing (ASAP-seq) and cellular indexing of transcriptomes and epitopes (CITE-seq) were performed on NK cells from the peripheral blood of HCMV-infected individuals with NKG2C+ NK cell expansions and HCMV-negative individuals. They employed cell surface protein information to designate clusters defined by transcriptomes and chromatin accessibility with existing NK cell subset classifications, while evaluating the correctness of these population definitions objectively.
Fig.3 Mapping NK cell subsets onto transcriptional and epigenetic landscapes. (Rückert, 2022)
They identified four main clusters in both modalities that could be designated as CD56-bright, early CD56-dim, mature CD56-dim, and adaptive NK cells, each with distinct genomics signatures consistent with previous findings. They also found an additional cluster of proliferating cells that were only visible through transcriptional profiling. Between CD56-bright and CD56-dim NK cells, there was a population of seemingly intermediate, early CD56-dim (CD16+ CD56- CD62L+ NKG2A+) NK cells that had characteristics of both subsets, such as high gene scores for TCF7, ZEB1, and ZBTB16.
Fig.4 Analyzing the transcriptional and epigenetic characteristics of different subsets of NK cells. (Rückert, 2022)
Result—Adaptive NK Cell Clonotypes Are Stably Maintained Over Time
Three HCMV-positive donors were monitored for 11, 7, and 19 months. Chromatin accessibility clusters were unchanged between time points, indicating that the frequency and makeup of the adaptive NK cell pool remained constant at the subcluster level. Additionally, subcluster-specific open chromatin areas remained unchanged. Importantly, the same clonotype-defining mutations were identified and connected with the original subclusters at both time points, confirming their longevity and the stability of adaptive subclusters as distinct clonal expansions. The total distribution of clonotypes remained stable over time, showing that the adaptive compartment-associated clonotypes maintained their frequencies.
Fig.5 Adaptive NK cell clonotypes are stably maintained over time. (Rückert, 2022)
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Reference
- Rückert, T.; et al. Clonal expansion and epigenetic inheritance of long-lasting NK cell memory. Nature Immunology. 2022, 23(11): 1551-1563.
