Common variations in the IL4R gene affect splicing and influence natural expression of the soluble isoform

We previously found the soluble interleukin 4 receptor (sIL4R) to be differently expressed in allergic asthma patients compared to healthy individuals. Here we present data demonstrating the involvement of the sequence variations, c.912-1003A > G, c.912-833T > C, c. 912-630A > G, and c.912-577A > G, in the expressional regulation of IL4R splice variants. By using an IL4R minigene construct, genomic DNA and mRNA from asthma patients and nonasthmatic individuals, we analyzed the function of four highly-linked SNPs, flanking the alternatively-spliced exon in the IL4R gene. Results from the minigene assay showed that the form containing the minor alleles significantly decreased the expression of the soluble IL4R (exon 8+) variant, a decrease that could only be seen in the major construct after increasing amounts of either the splicing factor SRp20, or YT521-B. Analysis of mRNA expression in our human material confirmed the results, demonstrating lower expression of the sIL4R in patients and controls carrying the minor alleles. Together these results show sequence variations as a possible way of altering alternative splicing selection of IL4R in vivo.     

A "silent" nucleotide substitution in exon 4 is responsible for the "alternative expression" of HLA-A*01:01:38L through aberrant splicing

A Welsh Bone Marrow Donor Registry donor was serologically typed, using both alloantisera and monoclonal antibodies, as human leukocyte antigen (HLA)-A2, A-, but typed by polymerase chain reaction sequence-specific priming as HLA-A*01, A*02. Full gene sequencing of the A*01 separated allele indicated an apparently normal A*01:01:01:01 apart from a silent change at nucleotide 705 in exon 4, codon 211 (alanine: normally GCG but GCA in this donor). Sequence analysis of the amplified A*01 allele in cDNA synthesized from RNA indicated that exons 1, 2, 3, and 5 had typical A*01:01 sequences. However, exon 4 was truncated in this allele (87 nucleotides shorter), beginning just after the single nucleotide polymorphism (SNP) identified in genomic DNA sequencing. The nucleotide sequence up to, and 1 nucleotide after, the SNP is homologous with the 3' end of human leukocyte antigen (HLA)-A intron 3 and thus resembles a splice site. However, a small amount of "normal" HLA-A1 was detected on the surface of cells from an Epstein-Barr virus transformed B-cell line (BCL), but not on peripheral blood mononuclear cells, by flow cytometry. Additionally, a trace amount of "normal sized" A*01 was amplified from cDNA. We suggest that in this A*01 variant allele (A*01:01:38L) intron 3 is largely spliced out with a part of exon 4; exon 4 is still in-frame but the protein is smaller than the wild type. This is likely to affect folding and assembly of the "wild type" mature protein on the cell surface, thus explaining the apparent null phenotype when assayed by conventional serology. However, a small amount of A1 protein is made from correctly spliced A*01 mRNA and is detectable on BCLs using flow cytometry.     

Improved T cell assay for identification of type 1 diabetes patients

Diabetes mellitus is comprised primarily of two clinically separate diseases: type 1 (T1D) and type 2 diabetes (T2D). T1D is a cell-mediated autoimmune disease directed against the beta cells and characterized by autoantibody (Ab) and T cell reactivity to islet proteins whereas, T2D is non-autoimmune. Despite the fact that the pathological process in autoimmune diabetes involves T cells, immune markers of diabetes have primarily centered on the presence of circulating serum islet autoantibodies. In two masked NIH sponsored workshops, our cellular immunoblotting T cell assay, which uses isolated human islets separated into 18 molecular weight fractions, has been validated to be able to distinguish T1D patients from controls with excellent specificity and sensitivity. In this study, we utilized the first workshop to select eight molecular weight fractions of human islets that were the most discriminatory between T1D patients and controls. Using these eight molecular weight fractions identified in the first workshop, we validated the preferential recognition of these 8 blot sections in a second workshop. We then re-calculated the sensitivity and specificity of the cellular immunoblotting assay for both workshops using only the data from these 8 blot sections. We observed increases in both sensitivity and specificity compared to the original workshop data for both workshops. The use of 8 instead of 18 molecular weight regions allows for a significant reduction in the amount of blood needed from patients, thus allowing cellular immunoblotting to be performed on pediatric patients participating in immunomodulatory studies. This improved T cell assay, which directly measures islet reactive T cell responses in autoimmune diabetes patients with excellent sensitivity and specificity, will likely improve patient follow-up during intervention studies.