Regulation of HLA class I expression by non-coding gene variations.

The Human Leukocyte Antigen (HLA) is a critical genetic system for different outcomes after solid organ and hematopoietic cell transplantation. Its polymorphism is usually determined by molecular technologies at the DNA level. A potential role of HLA allelic expression remains under investigation in the context of the allogenic immune response between donors and recipients. In this study, we quantified the allelic expression of all three HLA class I loci (HLA-A, B and C) by RNA sequencing and conducted an analysis of expression quantitative traits loci (eQTL) to investigate whether HLA expression regulation could be associated with non-coding gene variations. HLA-B alleles exhibited the highest expression levels followed by HLA-C and HLA-A alleles. The max fold expression variation was observed for HLA-C alleles. The expression of HLA class I loci of distinct individuals demonstrated a coordinated and paired expression of both alleles of the same locus. Expression of conserved HLA-A~B~C haplotypes differed in distinct PBMC's suggesting an individual regulated expression of both HLA class I alleles and haplotypes. Cytokines TNFα /IFNβ, which induced a very similar upregulation of HLA class I RNA and cell surface expression across alleles did not modify the individually coordinated expression at the three HLA class I loci. By identifying cis eQTLs for the HLA class I genes, we show that the non-coding eQTLs explain 29%, 13%, and 31% of the respective HLA-A, B, C expression variance in unstimulated cells, and 9%, 23%, and 50% of the variance in cytokine-stimulated cells. The eQTLs have significantly higher effect sizes in stimulated cells compared to unstimulated cells for HLA-B and HLA-C genes expression. Our data also suggest that the identified eQTLs are independent from the coding variation which defines HLA alleles and thus may be influential on intra-allele expression variability although they might not represent the causal eQTLs. Author summary: In transplantation, the allogenic immune response is linked to the HLA compatibility between donor and recipient, HLA genes being highly polymorphic. The impact of this allelic polymorphism on MHC cell surface expression and the potential role of expression in the T cell activation and on clinical outcomes remains poorly investigated. In this study, we documented the individual variability of allelic HLA class I expression in PBMCs by RNA sequencing. To mimic the inflammatory clinical situation after transplantation, we performed a similar analysis following cytokine (TNFα/IFNβ) stimulation of PBMCs. The results demonstrated a coordinated and paired expression of both alleles of the same locus in all individuals. The levels of expression of matched HLA-A~B~C haplotypes differed in distinct PBMCs suggesting that expression of both HLA class I alleles and haplotypes is regulated individually. To identify cis regulatory elements of expression we performed an eQTL analysis on unstimulated and stimulated PBMCs. These eQTLs accounted for up to 9%, 23% and 50% of the respective HLA-A, B and C expression variance in stimulated PBMCs. Of interest, we could show that they are independent from the SNPs encoding allelic variation, meaning that they could explain a different portion of the variance in HLA expression. [ABSTRACT FROM AUTHOR]