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. Most studies have focused on the vast allelic variation in these genes; only a few studies have explored differences in the expression levels of HLA alleles. In this study, we quantified mRNA expression levels of HLA class I and II genes from peripheral blood samples of 50 healthy individuals. The gene- and allele-specific mRNA expression was assessed using unique molecular identifiers, which enabled PCR bias removal and calculation of the number of original mRNA transcripts. We identified differences in mRNA expression between different HLA genes and alleles. Our results suggest that HLA alleles are differentially expressed and these differences in expression levels are quantifiable using RNA sequencing technology. Our method provides novel insights into HLA research, and it can be applied to quantify 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.
Highlights
The highly polymorphic human leukocyte antigens (HLA) are crucial in presentation of self, nonself and tumor antigens to T cells, and play an important part in autoimmunity and infection responses, as well as in organ and hematopoietic stem cell transplantation (HSCT)
To determine HLA gene- and allele-specific expression using unique molecular identifiers (UMIs), we developed an RNA sequencing (RNA-Seq) protocol (Figure 1) based on the STRT method [40]
Our method included an incorporation of 10 bp UMI to the 5’ end of RNA transcripts using a template switching oligo (TSO) in the first strand synthesis followed by an amplification of the full-length complementary DNA
Summary
The highly polymorphic human leukocyte antigens (HLA) are crucial in presentation of self, nonself and tumor antigens to T cells, and play an important part in autoimmunity and infection responses, as well as in organ and hematopoietic stem cell transplantation (HSCT). Recent studies have reported varying expression levels of HLA alleles based on the quantitative polymerase chain reaction (qPCR) [3,4,5,6,7,8,9] and the mean fluorescence intensity (MFI) [10, 11]. The differential expression of HLA genes and alleles has been associated with immunologically mediated diseases, such as Crohn’s disease [7] and HIV [11, 12], follicular
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
