Tuning of NK-Specific HLA-C Expression by Alternative mRNA Splicing.

Frederick J Goodson-Gregg,Victoria E Walker-Sperling,Amy Zhang,Hongchuan Li,Mary Carrington,Paul W Wright,Brian Rothbard,Stephen K Anderson

doi:10.3389/fimmu.2019.03034

Abstract

A complex system regulating HLA-C expression in NK cells, driven by an NK-specific promoter that produces alternatively spliced variants of the 5′-UTR has been recently identified. Exon content of the NK-specific 5′-UTR varies strikingly across HLA-C alleles, with some exons being allele specific. In order to investigate the possibility that allelic variation in the 5′-UTR modulates HLA-C expression levels, cDNAs containing several distinct classes of 5′-UTR were compared. Subtle changes in 5′-UTR content had a significant effect on the expression of HLA-C*03 and HLA-C*12 cDNA clones, suggesting that alternative splicing can fine-tune the level of protein expression. The HLA-C*06 allele was found to be highly expressed in relation to the other alleles studied. However, its increased expression was primarily associated with differences in the peptide-binding groove. Although the impact of allele-specific alternative splicing of NK-Pro transcripts on protein levels can be modest when compared with the effect of changes in peptide-loading, alternative splicing may represent an additional regulatory mechanism to fine-tune HLA-C levels within NK cells in distinct tissue environments or at different stages of maturation in order to achieve optimal levels of missing-self recognition.

Highlights

Natural Killer (NK) cells are innate immune cells that sense transformed and virally infected cells using an array of activating receptors [1]
In order to identify the patterns of 5′-UTR splicing for individual HLA-C alleles, we performed full-length RT-PCR on RNA isolated from purified peripheral blood NK cells from individuals that were homozygous for HLA-C∗03, HLA-C∗04, or HLA-C∗06
The previous identification of an HLA-C NK-specific promoter capable of generating a wide array of alternatively spliced mRNAs, as well as allele-specific splice variants, suggested that endogenous HLA-C expression may play an important role in NK cell activity or education [12]

Summary

Introduction

Natural Killer (NK) cells are innate immune cells that sense transformed and virally infected cells using an array of activating receptors [1]. The activation of NK cells is held in check by inhibitory receptors that recognize self MHC [2, 3]. As NK cells mature, they shift from utilizing CD94:NKG2A receptors that recognize the invariant HLA-E molecule, to KIR that recognize specific subsets of HLA class I molecules [4, 5]. There is variation in the expression level of individual HLA-C alleles, and increased levels of expression have been associated with improved outcomes in HIV infection [8]. Several distinct mechanisms have been shown to affect HLA-C expression levels: polymorphisms in transcription factor binding sites; peptide loading efficiency; miRNA interaction with the 3′-UTR [9,10,11]

Methods

Results

Conclusion