Trans-ancestral fine-mapping of MHC reveals key amino acids associated with spontaneous clearance of hepatitis C in HLA-DQβ1

Spontaneous clearance of acute hepatitis C virus (HCV) infection is associated with single nucleotide polymorphisms (SNPs) on the MHC class II. We fine-mapped the MHC region in European (n = 1,600; 594 HCV clearance/1,006 HCV persistence) and African (n = 1,869; 340 HCV clearance/1,529 HCV persistence) ancestry individuals and evaluated HCV peptide binding affinity of classical alleles. In both populations, HLA-DQβ1Leu26 (p value_Meta = 1.24 × 10^-14) located in pocket 4 was negatively associated with HCV spontaneous clearance and HLA-DQβ1Pro55 (p value_Meta = 8.23 × 10^-11) located in the peptide binding region was positively associated, independently of HLA-DQβ1Leu26. These two amino acids are not in linkage disequilibrium (r² < 0.1) and explain the SNPs and classical allele associations represented by rs2647011, rs9274711, HLA-DQB1^∗03:01, and HLA-DRB1^∗01:01. Additionally, HCV persistence classical alleles tagged by HLA-DQβ1Leu26 had fewer HCV binding epitopes and lower predicted binding affinities compared to clearance alleles (geometric mean of combined IC₅₀ nM of persistence versus clearance; 2,321 nM versus 761.7 nM, p value = 1.35 × 10^-38). In summary, MHC class II fine-mapping revealed key amino acids in HLA-DQβ1 explaining allelic and SNP associations with HCV outcomes. This mechanistic advance in understanding of natural recovery and immunogenetics of HCV might set the stage for much needed enhancement and design of vaccine to promote spontaneous clearance of HCV infection.

First genotype-phenotype study reveals HLA-DQβ1 insertion heterogeneity in high-resolution manometry achalasia subtypes

Background

Achalasia is a primary oesophageal motility disorder. Although aetiology remains mainly unknown, a genetic risk variant, rs28688207 in HLA-DQB1, showed strong achalasia association suggesting involvement of immune-mediated processes in the pathogenesis. High-resolution manometry recognises three types of achalasia. The aim of our study was to perform the first genotype-phenotype analysis investigating the frequency of rs28688207 across the high-resolution manometry subtypes.

Methods

This was a cross-sectional retrospective study. Achalasia patients from tertiary centres in the Czech Republic (n = 163), Germany (n = 114), Greece (n = 70) and controls were enrolled. All subjects were genotyped for the rs28688207 insertion. The Kruskal-Wallis test was used for the genotype-phenotype analysis.

Results

A total of 347 achalasia patients (type I - 89, II - 210, III - 48) were included. The overall frequency of the rs28688207 was 10.3%. The distribution of the insertion was significantly different across the high-resolution manometry subtypes (p = 0.038), being most prevalent in type I (14.6%), followed by type II (9.5%) and III (6.3%).

Conclusion

The frequency of the HLA-DQB1 insertion differs among high-resolution manometry achalasia subtypes. The insertion is most prevalent in type I, suggesting that immune-mediated mechanisms triggered by the insertion may play a more prominent role in the pathogenesis of this subtype.

Frequency of HLA DQβ1*0201 and DQβ1*0301 Alleles and Total Serum IgE in Patients with Bronchial Asthma: A Pilot Study from Pakistan

In Pakistan about 3.7% of the population is suffering from asthma, a chronic inflammatory disorder of airways. Asthma has wide spectrum of predisposing factors including environment and genetics. Many studies have been performed to determine association of asthma with serum IgE and major histocompatibility complex (MHC) alleles but conflicting results were reported. Therefore, present study was designed to determine frequency of HLA-DQβ1*0201 and DQβ1*0301 alleles in patients with bronchial asthma. This case control study included 85 asthmatic patients and 85 healthy controls. HLA-DQβ1*0201 and DQβ1*0301 alleles were detected by allele specific PCR and serum IgE was determined by ELISA. Median and inter-quartile range (IQR) of total IgE level were more increased in asthma patients (585.7 IU/mL and 247.2-848.1 IU/mL) compared to healthy controls (65.1 IU/mL and 28.1-181.3 IU/mL) (p<0.001). Frequency of HLA-DQβ1*0201 and -DQβ1*0301 alleles was more in healthy controls (32% and 38%, p=0.616) as compared to bronchial asthma patients (28% and 26%, p= 0.09). There was a significant association of IgE levels and HLA-DQβ1*0201 allele. Patients positive for HLA-DQβ1*0201 allele had low level of serum IgE 357.2 IU/mL (153.9-634.3 IU/mL) compared to the patients negative for this HLA allele i.e. 642.9 IU/mL (289.8-1299.5IU/mL) (p=0.005), whereas, HLA-DQβ1*0301 allele was not associated with total serum IgE level (p=0.865). Our findings show that HLA-DQβ1*0201 and -DQβ1*0301 alleles were not associated with asthma; however, HLA-DQβ1*0201 allele was associated with low levels of total serum IgE in the study population.