Identification of an elaborate NK-specific system regulating HLA-C expression

The HLA-C gene appears to have evolved in higher primates to serve as a dominant source of ligands for the KIR2D family of inhibitory MHC class I receptors. The expression of NK cell-intrinsic MHC class I has been shown to regulate the murine Ly49 family of MHC class I receptors due to the interaction of these receptors with NK cell MHC in cis. However, cis interactions have not been demonstrated for the human KIR and HLA proteins. We report the discovery of an elaborate NK cell-specific system regulating HLA-C expression, indicating an important role for HLA-C in the development and function of NK cells. A large array of alternative transcripts with differences in intron/exon content are generated from an upstream NK-specific HLA-C promoter, and exon content varies between HLA-C alleles due to SNPs in splice donor/acceptor sites. Skipping of the first coding exon of HLA-C generates a subset of untranslatable mRNAs, and the proportion of untranslatable HLA-C mRNA decreases as NK cells mature, correlating with increased protein expression by mature NK cells. Polymorphism in a key Ets-binding site of the NK promoter has generated HLA-C alleles that lack significant promoter activity, resulting in reduced HLA-C expression and increased functional activity. The NK-intrinsic regulation of HLA-C thus represents a novel mechanism controlling the lytic activity of NK cells during development.
Author summary It has been proposed that the human HLA-C gene evolved in higher primates to serve as a ligand for the KIR family of inhibitory receptors for MHC class I that are expressed by natural killer (NK) cells and regulate their activity. NK cell potential is determined by the level of MHC class I on surrounding cells and on the NK cell itself. We have uncovered a highly complex system regulating HLA-C expression in NK cells. A NK-specific promoter produces a large array of differentially-spliced transcripts that vary in their ability to be translated into HLA-C protein. As NK cells differentiate and become more cytotoxic, the level of HLA-C expression increases, and this correlates with an increased abundance of translatable HLA-C mRNAs. A subset of HLA-C alleles have a promoter polymorphism that abrogates its activity, resulting in NK cells that are unable to upregulate HLA-C levels, and consequently, possess increased functional activity. Overall, our findings provide insight into the mechanisms of NK cell development, as well as a method to identify individuals with high NK activity, that may provide superior outcomes in hematopoietic stem cell transfer.