HLA RNAseq reveals high allele-specific variability in mRNA expression

Abstract

The HLA gene complex is the most important, single genetic factor in susceptibility to most diseases with autoimmune or autoinflammatory origin and in transplantation matching. The majority of the studies have focused on the huge allelic variation in these genes; only a few studies have explored differences in expression levels of HLA alleles. To study the expression levels of HLA alleles more systematically we utilised two different RNA sequencing methods. Illumina RNAseq has a high sequencing accuracy and depth but is limited by the short read length, whereas Oxford Nanopores technology can sequence long templates, but has a poor accuracy. We studied allelic mRNA levels of HLA class I and II alleles from peripheral blood samples of 50 healthy individuals. The results demonstrate large differences in mRNA expression levels between HLA alleles. The method can be applied to quantitate the expression differences of HLA alleles in various tissues and to evaluate the role of this type of variation in transplantation matching and susceptibility to autoimmune diseases.\n\nAuthor SummaryEven though HLA is widely studied less is known of its allele-specific expression. Due to the pivotal role of HLA in infection response, autoimmunity, and transplantation biology its expression surely must play a part as well. In hematopoietic stem cell transplantation the challenge often is to find a suitable HLA-matched donor due to the high allelic variation. Classical HLA typing methods do not take into account HLA allele-specific expression. However, differential allelic expression levels could be crucial in finding permissive mismatches in order to save a patients life. Additionally, differential HLA expression levels can lead into beneficial impact in viral clearance but also undesirable effects in autoimmune diseases. To study HLA expression we developed a novel RNAseq-based method to systematically characterize allele-specific expression levels of classical HLA genes. We tested our method in a set of 50 healthy individuals and found differential expression levels between HLA alleles as well as interindividual variability at the gene level. Since NGS is already well adopted in HLA research the next step could be to determine HLA allele-specific expression in addition to HLA allelic variation and HLA-disease association studies in various cells, tissues, and diseases.