HLA-G Haplotypes Are Differentially Associated with Asthmatic Features

Abstract

Human leukocyte antigen (HLA)-G, a HLA class Ib molecule, interacts with receptors on lymphocytes such as T cells, B cells, and natural killer cells to influence immune responses. Unlike classical HLA molecules, HLA-G expression is not found on all somatic cells, but restricted to tissue sites, including human bronchial epithelium cells (HBEC). Individual variation in HLA-G expression is linked to its genetic polymorphism and has been associated with many pathological situations such as asthma, which is characterized by epithelium abnormalities and inflammatory cell activation. Studies reported both higher and equivalent soluble HLA-G (sHLA-G) expression in different cohorts of asthmatic patients. In particular, we recently described impaired local expression of HLA-G and abnormal profiles for alternatively spliced isoforms in HBEC from asthmatic patients. sHLA-G dosage is challenging because of its many levels of polymorphism (dimerization, association with β2-microglobulin, and alternative splicing), thus many clinical studies focused on HLA-G single-nucleotide polymorphisms as predictive biomarkers, but few analyzed HLA-G haplotypes. Here, we aimed to characterize HLA-G haplotypes and describe their association with asthmatic clinical features and sHLA-G peripheral expression and to describe variations in transcription factor (TF) binding sites and alternative splicing sites. HLA-G haplotypes were differentially distributed in 330 healthy and 580 asthmatic individuals. Furthermore, HLA-G haplotypes were associated with asthmatic clinical features showed. However, we did not confirm an association between sHLA-G and genetic, biological, or clinical parameters. HLA-G haplotypes were phylogenetically split into distinct groups, with each group displaying particular variations in TF binding or RNA splicing sites that could reflect differential HLA-G qualitative or quantitative expression, with tissue-dependent specificities. Our results, based on a multicenter cohort, thus support the pertinence of HLA-G haplotypes as predictive genetic markers for asthma.

Keywords: alternative splicing; asthma; haplotypes; human leukocyte antigen-G; phylogeny; regulatory regions; transcription factor binding site.

Figure 1

Phylogenetic relationship between human leukocyte antigen-G (HLA-G) allele-haplotype sequences. The phylogenetic tree contains 19 sequences from −1983 to +3447 aligned using the multiple sequence alignment tool MUSCLE in the Molecular Evolutionary Genetics Analysis software version 7.0; sequences were H01-UTR1-G*01:01:01:01, H05-UTR1-G*01:01:01:01, H54-UTR1-G*01:01:01:01, H04-UTR4-G*01:01:01:05, H02-UTR4-G*01:01:01:05, H21-UTR5-G*01:03:01:02, H20-UTR5-G*01:03:01:02, H19-UTR5-G*01:03:01:02, H10-UTR2-G*01:01:02:01, H10-UTR2-G*01:01:02:02, H10-UTR2-G*01:06, H10-UTR2-G*01:05N, H23-UTR3-G*01:04:01, H23-UTR3-G*01:04:04, H16-UTR7G*01:01:03:03, H46-UTR6-G*01:01:01:01, H47-UTR6-G*01:01:01:04, H03-UTR6-G*01:01:01:04, and H49-UTR6-G*01:01:01:06. Evolutionary relationships among HLA-G whole sequences were inferred using the neighbor-joining method with 1,000 replicates. Evolutionary distances were computed using the p-distance method, and units were the number of base differences per site. The percentage of trees in which the associated taxa clustered together is shown next to the branches. The sum of branch length equals 0.01616800 base differences per site. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test is shown next to the branches. The tree was drawn to scale, with branch lengths in the same units (base differences per site) as the evolutionary distances used to construct the phylogenetic tree. Analysis involved gorilla HLA-G genomic sequence as an outgroup (accession number CU104658.1).