Sequence-specific oligonucleotide typing in Shona patients with rheumatoid arthritis and healthy controls from Zimbabwe

Indonesians Human Leukocyte Antigen (HLA) Distributions and Correlations with Global Diseases

In Human, Major Histocompatibility Complex known as Human Leukocyte Antigen (HLA). The HLA grouped into three subclasses regions: the class I region, the class II region, and the class III region. There are thousands of polymorphic HLAs, many of them are proven to have correlations with diseases. Indonesia consists of diverse ethnicity people and populations. It carries a unique genetic diversity between one and another geographical positions. This paper aims to extract Indonesians HLA allele data, mapping the data, and correlating them with global diseases. From the study, it is found that global diseases, like Crohn's disease, rheumatoid arthritis, Graves' disease, gelatin allergy, T1D, HIV, systemic lupus erythematosus, juvenile chronic arthritis, and Mycobacterial disease (tuberculosis and leprosy) suspected associated with the Indonesian HLA profiles.

A Comparative Analysis of the Peptide Repertoires of HLA-DR Molecules Differentially Associated With Rheumatoid Arthritis

OBJECTIVE

To evaluate similarity of the peptide repertoires bound to HLA-DR molecules that are differentially associated with rheumatoid arthritis (RA), and to define structural features of the shared peptides.

METHODS

Peptide pools bound to HLA-DRB1*01:01, HLA-DRB1*04:01, and HLA-DRB1*10:01 (RA associated) and those bound to HLA-DRB1*15:01 (non-RA-associated) were purified and analyzed by liquid chromatography (LC) matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MS) and LC-ion-trap MS. Peptide pools from each allotype were compared in terms of size, protein origin, composition, and affinity (both theoretical and experimental with some peptides). Finally, 1 peptide sequenced from DR1, DR4, and DR10, but not from DR15, was modeled in complex with all 4 HLA-DRB1 molecules and HLA-DRB5*01:01.

RESULTS

A total of 6,309 masses and 962 unique peptide sequences were compared. DR10 shared 29 peptides with DR1, 9 with DR4, and 1 with DR15; DR1 shared 6 peptides with DR4 and 9 with DR15; and DR4 and DR15 shared 4 peptides. The direct identification of peptide ligands indicated that DR1 and DR10 were the most similar molecules regarding the peptides that they could share. The peptides common to these molecules contained a high proportion of Leu at P4 and basic residues at P8 binding core positions.

CONCLUSION

The degree of overlap between peptide repertoires associated with different HLA-DR molecules is low. The repertoires associated with DR1 and DR10 have the highest similarity among the molecules analyzed (∼10% overlap). Among the peptides shared between DR1 and DR10, a high proportion contained Leu(4) and basic residues at the P8 position of the binding core.

Meta-analyses of the association of HLA-DRB1 alleles with rheumatoid arthritis among Arabs

AIM

Various studies incorporating Arab populations have reported on specific associations between HLA-DRB1 variants and rheumatoid arthritis (RA). We sought to provide an overview on the association of HLA-DRB1 with RA in Arabs using meta-analysis tools.

METHODS

Data on allele counts and frequencies were compiled from the relevant literature (published before 16 February 2016) and the associations of 13 -DRB1 variants with RA were assessed; relationships were defined in terms of odds ratios (ORs) with a 95% confidence interval.

RESULTS

Based on a collection of six studies, risk conferring or protective allele associations were derived from allele counts in 475 RA patients and 1213 controls. Two HLA-DRB1 alleles (-DRB1*04, *10) significantly conferred an increased risk for RA (OR > 2; P < 0.0001). Conversely, four alleles (-DRB1*03, *07, *11 and *13) significantly conferred a protective effect against RA (OR < 1; P < 0.05). No significant associations with RA were found for seven -DRB1 variants (-DRB1*01, *08, *09, *12, *14, *15 and *16).

CONCLUSION

With increased statistical power and effect size over individual studies, we present a more robust profile on the association of HLA-DRB1 variants with RA in the Arab ethnicity, and contribute to the global geo-ethnic picture in this context.

HLA-DRB1 and -DQB1 loci in three west African ethnic groups: genetic relationship with sub-Saharan African and European populations

The Fulani of west Africa have been shown to be less susceptible to malaria and to mount a stronger immune response to malaria than sympatric ethnic groups. The analysis of HLA diversity is useful for the assessment of the genetic distance between the Fulani and sympatric populations, which represents the necessary theoretical background for the investigation of genetic determinants of susceptibility to malaria. We assessed the polymorphism of HLA-DRB1 and -DQB1 loci and analyzed the distribution of alleles/haplotypes in Fulani, Mossi, and Rimaibé from Burkina Faso. We then investigated the genetic relationship of these three ethnic groups with other sub-Saharan African populations as well as with Europeans. We confirmed that the Fulani from Burkina Faso are genetically distinct from sympatric Mossi and Rimaibé. Furthermore the Fulani from Burkina Faso are close to those from The Gambia and, intriguingly, share the distribution of specific alleles with east African populations (Amhara and Oromo). It is noteworthy that the HLA-DRB1*04 and -DQB1*02 alleles, which are implicated in the development of several autoimmune diseases, are present at high frequency in the Fulani, suggesting their potential involvement in the enhanced immune reactivity observed in this population.

The rheumatoid arthritis-associated allele HLA-DR10 (DRB1*1001) shares part of its repertoire with HLA-DR1 (DRB1*0101) and HLA-DR4 (DRB*0401)

OBJECTIVE

To identify the peptide anchor motif for the rheumatoid arthritis (RA)-related HLA allele, DR10, and find shared natural ligands or sequence similarities with the other disease-associated alleles, DR1 and DR4.

METHODS

The HLA-DR10-associated peptides were purified, and a proportion of these natural ligands were de novo sequenced by mass spectrometry. Based on crystallographic structures, the complexes formed by peptide influenza virus hemagglutinin HA306-318 with DR1, DR4, and DR10 were modeled, and binding scores were obtained.

RESULTS

A total of 238 peptides were sequenced, and the anchor motif of the HLA-DR10 peptide repertoire was defined. A large proportion of the DR10-associated peptides had the structural features to bind DR1 and DR4 but were theoretical nonbinders to the negatively associated alleles DR15 and DR7. Among the sequenced ligands, 10 had been reported as ligands to other RA-associated alleles. Modeling data showed that peptide HA306-318 can bind DR1, DR4, and DR10 with similar affinities.

CONCLUSION

The data show the presence of common peptides in the repertoires of RA-associated HLA alleles. The combination of the shared epitope present in DR1, DR4, and DR10 together with common putative arthritogenic peptide(s) could influence disease onset or outcome.

HLA class II disease associations in southern Africa

Southern Africa harbors several population groups representing a diversity of gene pool origins. This provides a unique opportunity to study genetic disease predisposition in these populations against a common environmental background. Human leukocyte antigen (HLA) association studies of these populations could improve knowledge on inter-population variation and HLA-related disease susceptibility. The aim of this paper is to review HLA class II disease associations reported for southern African population groups, compare them with findings in other populations and identify those unique to southern Africa. A number of HLA class II disease associations appear to be unique to southern African populations. These include DRB1*14011 association with insulin-dependent diabetes mellitus susceptibility in the Xhosa and DRB1*10 and DQB1*0302 with rheumatoid arthritis susceptibility in the South African (SA) Indian and SA Coloreds, respectively. A noteworthy similarity in class II disease association was observed among southern African Caucasoid and their European parental populations. Unique HLA class II disease associations observed in southern Africa are consistent with the notion that unique environmental and natural selective factors have resulted in certain ethnic-specific HLA class II disease associations, while common HLA class II disease associations found across different populations support the notion that common diseases are caused by common, ancient alleles present in indigenous African populations.

Rheumatic diseases in minority populations

Rheumatic diseases are expressed in all ethnic populations, but differ in prevalence, genetic associations, clinical features, and responses to interventions. Most data describing these differences do so in reference to and comparisons with white populations. These are sparse data that evaluate differences within minority populations where there is more homogeneity of external factors, such as social, cultural, and behavioral attitudes. This article reviews the features that are unique to various rheumatic diseases within minority populations.

Heterogeneity between men and women in the influence of the HLA-DRB1 shared epitope on the clinical expression of rheumatoid arthritis

OBJECTIVE

To test the hypothesis that the influence of the HLA-DRB1 shared epitope (SE) on the clinical manifestations of rheumatoid arthritis (RA) differs between men and women.

METHODS

We assessed 777 consecutive RA patients for age at disease onset, articular manifestations, subcutaneous nodules, laboratory and radiographic findings, and treatment received. We typed HLA-DRB1 alleles by polymerase chain reaction-sequence-specific primer amplification and categorized the number of SE-containing alleles. We used regression models to adjust comparisons between the sexes for age and clustering by recruitment center, and included SE x sex interaction terms to look for heterogeneity between men and women in the effect of the SE.

RESULTS

Among the 777 RA patients, 548 (71%) were women. Men and women differed significantly in the adjusted frequency of SE positivity (women 71.4% versus men 78.4%; P < or = 0.001). The SE was associated with a younger age at symptom onset and RA diagnosis among men, but not among women. The SE likewise had a significant adverse effect on joint tenderness, swelling, and deformity among men only. The SE was associated with a higher erythrocyte sedimentation rate in women and more frequent positivity for rheumatoid factor among both men and women.

CONCLUSION

There is heterogeneity between men and women in the effect of the SE on RA susceptibility and clinical expression. Further research is needed to understand the mechanism of this heterogeneity.

The shared epitope and severity of rheumatoid arthritis

After two decades of research involving thousands of RA patients, it is still not possible to precisely define the relation of HLA-DRB1 SE alleles to RA severity. Improvements in our understanding require more careful consideration of several factors such as ethnicity, gender, and the specific SE allele and genotype inherited. Large studies of heterogeneous groups of patients are required and indicate the need for collaborative efforts among researchers. In the interim, meta-analysis of the existing literature may provide some insight, because it allows utilization of the tremendous amount of research already completed. A preliminary meta-analysis highlighted the significant heterogeneity among the existing literature, and a more ambitious meta-analysis that uses individual patient-level data is currently ongoing. Profound implications exist for determination of the precise relationship between the SE and RA severity. This information could be valuable in identifying patients at greater risk of severe complications or as a stratification variable for clinical trials. Moreover, patients genetically predisposed to severe disease may benefit from early initiation of more aggressive therapy. Ultimately, clarification of the role of the SE may be valuable for the development of specific therapies directed toward DRB1 and related targets.

HLA-DRB1 alleles associated with susceptibility or resistance to rheumatoid arthritis, articular deformities, and disability in Mexican Americans

OBJECTIVE

To study the genetics (HLA-DRB1 allele associations) of rheumatoid arthritis (RA) susceptibility and severity among Mexican Americans, an important, but understudied, US population.

METHODS

HLA-DRB1 alleles were compared between 141 Mexican American patients with RA and 54 unrelated Mexican Americans without RA, and the association of these alleles with articular deformities and disability was examined. HLA-DRB1 alleles were typed using polymerase chain reaction-sequence-specific primer amplification and were classified according to the 1996 World Health Organization nomenclature.

RESULTS

Of the 141 patients, 105 (74%) had at least 1 copy of the shared epitope (SE) sequence, compared with 29 (54%) of the 54 controls (P = 0.007). A significant gene-dose effect was observed, with 31 patients (22%) being homozygous for the SE compared with 1 (2%) of the controls (P = 0.004). In terms of disease severity, only 3% of RA patients who were "null" for the SE were outliers in the rate of development of articular deformities, compared with 10% of heterozygotes and 27% of homozygotes (P = 0.002). Patients who were DRB1*08 positive had significantly fewer deformities per year of disease and a slower rate of development of disability than did patients with other DRB1 alleles.

CONCLUSION

HLA-DRB1 alleles containing the SE are associated with susceptibility to RA in Mexican Americans, and may also be associated with a more rapid development of articular deformities and disability. HLA-DRB1*08 appears to have a protective influence on RA susceptibility and disease severity in Mexican Americans.

The HLA-DQ7 and -DQ8 associations in DR4-positive rheumatoid arthritis patients. A combined analysis of data available in the literature

Several different lines of evidence have demonstrated that inherited susceptibility to rheumatoid arthritis (RA) is associated with the DRB1 genes encoding the HLA-DR4 and HLA-DR1 molecules. A contrasting hypothesis has recently been proposed, suggesting that, in general, the DRB1 locus is associated with protection to RA and that the RA-associated DRB1 alleles are not responsible for the primary disease association but merely permissive for the susceptibility conferred by the HLA-DQ alleles with which they are in linkage disequilibrium. We have performed a critical review of the literature on the HLA association in RA with special emphasis on studies in which both an HLA-DR and -DQ association has been investigated. Our analyses provide strong evidence against the hypothesis that HLA-DQ molecules play a major role in the general susceptibility to RA. Thus, the strongest association in rheumatoid arthritis is with DRB1 genes rather than DQB1 genes.

[HLA-DRB1 and HLA-DQB1 polymorphism in Algerians from Algiers]

The polymorphism of HLA-DRB1 and HLA-DQB1 genes in 100 unrelated Algerians from Alger was investigated using PCR amplification and oligonucleotide typing. Compared to western Europeans, this population shows a higher haplotypic frequency of HLA DRB1*03-DQB1*0201 (21.5%) and a lower haplotypic frequency of DRB1*0101-DQB1*0501 (2%). Two unexpected haplotypes are observed: DRB1*07-DQB1*0301 and DRB1*0406-DQB1*0402. DRB1*0402 is the most common subtype in the DRB1*04 group. Furthermore, we detected a rare DQB1*0305 allele, only found in a Sardinian subject until today.

Cellular immune mechanisms in rheumatoid arthritis and other inflammatory arthritides

Advances in molecular genetics, cellular immunology and microbiology have offered promise in unravelling the aetiopathogenesis of inflammatory arthritides such as rheumatoid arthritis and reactive arthritis. Such insights are challenging the orthodox view that these diseases are primarily autoimmune in nature, and should lead to exciting and novel therapeutic approaches.