A major goal of this work was to define, from the transcriptome-wide perspective, the NK cells in various states to generate novel insights and a resource describing the specific genes involved with NK cell functions. We used the breadth of cell populations available from the ImmGen project to explore transcripts that define the identity of NK cells in a more robust and in-depth perspective than provided by previous analyses10–12
. The results show extensive transcriptional differences between NK cells and other leukocyte populations far beyond the few specific markers commonly used to identify them by flow cytometry. In addition, we found that few transcripts were uniquely specific to NK cells, many being shared with other cell types of the immune system, particularly T cells. These data provide a genome-wide context for interpretation of NK cell functions and will accelerate the discovery of pathways that regulate NK cell activation states.
We demonstrate a close transcriptional relatedness between naïve NK cells and innate-like T cells, suggesting that their gene expression profiles reflect a functional rather than developmental similarity. The abundance of cell surface receptors and signaling molecules expressed in NK and innate-like T cells is consistent with their role as a primary sentinel and reveals a wealth of novel signaling mechanisms for further targeted exploration.
Although NK cells are distinct in their innate properties, they also exhibit properties associated with adaptive CD8+ T cells including cytotoxicity and memory. Our work provides the first systematic identification of the genes associated with these common behaviors and identifies hundreds of genes not previously known to be associated with these functions. We found elements of the effector and memory NK cell differentiation signature that were shared by effector and memory CD8+ T cells, suggesting conservation of some activation mechanisms between NK and CD8+ T cell lineages. However, this must be interpreted in the context of dynamic changes in activation state, as evidenced by distinct NK cell transcriptomes at each stage of differentiation from naïve to activated to late effector to memory cell. Although understanding the function of NK cell memory is in its infancy, one implication of a defined gene expression signature corresponding to memory differentiation is that specific genes could be useful as surrogate markers for memory NK cells with the greatest potential to confer immunologic potential.
As for αβ T cells, the memory NK cell differentiation signature contains genes that are both unique to the memory state (e.g. Casp1, Fasl, and Ly6c1) and genes that are initially expressed in effector cells and are maintained in memory cells (e.g. Itga1 and Hopx) – genes that have not been previously appreciated for a potential role in NK cell memory and worthy of further study. This suggests that the transcriptome of memory NK cells represents a composite of genes uniquely expressed by these long-lived cells and those maintained from prior stages of differentiation, possibly to allow quick re-expression upon secondary exposure to antigen. We speculate that the expression pattern of the memory “repertoire”, rather than the individual genes themselves, is required to define the memory NK cell state.
This study provides a comprehensive transcriptome perspective on various stages of NK cell function in the context of closely related T lymphocytes. The data simultaneously support and extend previous findings, while providing a unique resource for future investigation of NK cell biology.