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

Area of Science:

• Immunogenetics
• Molecular Biology
• Genomics

Background:

• The Human Leukocyte Antigen (HLA) system is crucial for transplantation outcomes.
• HLA polymorphism is typically assessed at the DNA level.
• The role of HLA allelic expression in allogeneic immune responses requires further investigation.

Purpose of the Study:

• To quantify the allelic expression of HLA class I loci (HLA-A, B, C) using RNA sequencing.
• To investigate the association between HLA expression regulation and non-coding gene variations via eQTL analysis.
• To determine the impact of cytokines on HLA class I expression and coordinated regulation.

Main Methods:

• RNA sequencing was employed to quantify allelic expression of HLA-A, HLA-B, and HLA-C.
• Expression quantitative trait loci (eQTL) analysis was performed to identify regulatory genetic variations.
• Peripheral blood mononuclear cells (PBMCs) were stimulated with TNFα/IFNβ to assess cytokine effects.

Main Results:

• HLA-B alleles showed the highest expression, followed by HLA-C and HLA-A, with HLA-C exhibiting the greatest fold variation.
• Coordinated and paired expression of alleles within the same HLA locus was observed, differing between individuals and haplotypes.
• Non-coding cis-eQTLs explained significant portions of HLA expression variance (29% for HLA-A, 13% for HLA-B, 31% for HLA-C in unstimulated cells; 9%, 23%, 50% respectively in stimulated cells).
• eQTLs had larger effect sizes in cytokine-stimulated cells for HLA-B and HLA-C, suggesting enhanced regulatory influence.

Conclusions:

• HLA class I expression is individually regulated at both allelic and haplotype levels.
• Cytokine stimulation upregulates HLA class I expression but does not alter the coordinated individual expression patterns.
• Identified eQTLs, independent of coding variation, contribute to intra-allele expression variability and may not be the causal variants.