Investigating the genetic makeup of the major histocompatibility complex (MHC) in the United Arab Emirates population through next-generation sequencing

The Human leukocyte antigen (HLA) molecules are central to immune response and have associations with the phenotypes of various diseases and induced drug toxicity. Further, the role of HLA molecules in presenting antigens significantly affects the transplantation outcome. The objective of this study was to examine the extent of the diversity of HLA alleles in the population of the United Arab Emirates (UAE) using Next-Generation Sequencing methodologies and encompassing a larger cohort of individuals. A cohort of 570 unrelated healthy citizens of the UAE volunteered to provide samples for Whole Genome Sequencing and Whole Exome Sequencing. The definition of the HLA alleles was achieved through the application of the bioinformatics tools, HLA-LA and xHLA. Subsequently, the findings from this study were compared with other local and international datasets. A broad range of HLA alleles in the UAE population, of which some were previously unreported, was identified. A comparison with other populations confirmed the current population's unique intertwined genetic heritage while highlighting similarities with populations from the Middle East region. Some disease-associated HLA alleles were detected at a frequency of > 5%, such as HLA-B*51:01, HLA-DRB1*03:01, HLA-DRB1*15:01, and HLA-DQB1*02:01. The increase in allele homozygosity, especially for HLA class I genes, was identified in samples with a higher level of genome-wide homozygosity. This highlights a possible effect of consanguinity on the HLA homozygosity. The HLA allele distribution in the UAE population showcases a unique profile, underscoring the need for tailored databases for traditional activities such as unrelated transplant matching and for newer initiatives in precision medicine based on specific populations. This research is part of a concerted effort to improve the knowledge base, particularly in the fields of transplant medicine and investigating disease associations as well as in understanding human migration patterns within the Arabian Peninsula and surrounding regions.

HLA pharmacogenetic markers of drug hypersensitivity from the perspective of the populations of the Greater Middle East

Specific HLA associations with drug hypersensitivity may vary between geographic regions and ethnic groups. There are little to no data related to HLA-drug hypersensitivity on populations who reside in the Greater Middle East (GME), a vast region spanning from Morocco in the west to Pakistan in the east. In this review, the authors intended to summarize the significant HLA alleles associated with hypersensitive drug reactions induced by different drugs, as have been found in different populations, and to summarize the prevalence of these alleles in the specific and diverse populations of the GME. For example, HLA-B*57:01 allele prevalence, associated with abacavir-induced hypersensitivity, ranges from 1% to 3%, and HLA-DPB1*03:01 prevalence, associated with aspirin-induced asthma, ranges from 10% to 14% in the GME population. Studying pharmacogenomic associations in the ethnic groups of the GME may allow the discovery of new associations, confirm ones found with a low evidence rate and enable cost-effectiveness analysis of allele screening before drug use.

Abacavir usage patterns and hypersensitivity reactions in the EuroSIDA cohort

OBJECTIVES

Five to eight per cent of HIV-positive individuals initiating abacavir (ABC) experience potentially fatal hypersensitivity reactions (HSRs). We sought to describe the proportion of individuals initiating ABC and to describe the incidence and factors associated with HSR among those prescribed ABC.

METHODS

We calculated the proportion of EuroSIDA individuals receiving ABC-based combination antiretroviral therapy (cART) among those receiving cART after 1 January 2009. Poisson regression was used to identify demographic, and current clinical and laboratory factors associated with ABC utilization and discontinuation.

RESULTS

Between 2009 and 2016, of 10 076 individuals receiving cART, 3472 (34%) had ever received ABC-based cART. Temporal trends of ABC utilization were also heterogeneous, with 28% using ABC in 2009, dropping to 26% in 2010 and increasing to 31% in 2016, and varied across regions and over time. Poisson models showed lower ABC utilization in older individuals, and in those with higher CD4 cell counts, higher cART lines, and prior AIDS. Higher ABC utilization was associated with higher HIV RNA and poor renal function, and was more common in Central-East and Eastern Europe and lowest during 2014. During 779 person-years of follow-up (PYFU) in 2139 individuals starting ABC after 1 January 2009, 113 discontinued ABC within 6 weeks of initiation for any reason [incidence rate (IR) 14.5 (95% confidence interval (CI) 12.1, 17.5) per 100 PYFU], 13 because of reported HSR [IR 0.3 (95% CI 0.1, 1.0) per 100 PYFU] and 35 because of reported HSR/any toxicity [IR 4.5 (95% CI 3.2, 6.3) per 100 PYFU]. There were no factors significantly associated with ABC discontinuation because of reported HSR/any toxicity.

CONCLUSIONS

ABC remains commonly used across Europe and the incidence of discontinuation because of reported HSR was low in our study population.

Prevalence of abacavir-associated hypersensitivity syndrome and HLA-B*5701 allele in a Portuguese HIV-positive population

Background

Human Immunodeficiency Virus (HIV)-positive patients treated with the antiretroviral drug abacavir (ABC) may develop a potentially fatal ABC-associated hypersensitivity syndrome (ABC-HS), typically characterized by fever, malaise, rash, vomiting/diarrhoea and/or dyspnoea/cough. ABC-HS has been strongly associated with HLA-B*57:01 carriage and screening for this allele is recommended.

Objective

To determine the prevalence of HLA-B*57:01 and to characterize suspected ABC-HS in the adult HIV population from our hospital during a 7-year period.

Methods

Clinical data on patients under ABC treatment from January 2006 to December 2012 were analyzed to search for symptoms of ABC-HS. Reactions of suspected ABC-HS were characterized. HLA-B*57:01 and patch tests (1% and 10% ABC in petrolatum) with readings at 48 h were performed in those without previous testing. From January 2008 routine HLA-B*57:01 screening was implemented.

Results

From January 2006 to December 2007, 186 patients began treatment with ABC (data from 163 were available): 7 (4%) patients stopped ABC for suspected ABC-HS (71% males, median age 45 years) and the median time for onset of the reaction after starting ABC was 7 days. Four of the 7 patients had the HLA-B*57:01 allele and 2 of these 4 had positive patch tests. After HLA-B*57:01 screening implementation (January 2008), 573 patients were evaluated and 35 (6.1%) were HLA-B*57:01 positive; no suspected ABC-HS were observed since then.

Conclusion

Four patients with suspected ABC-HS (of 6 screened) were HLA-B*57:01 positive. No ABC-HS occurred since January 2008, after HLA-B*57:01 screening was implemented.

Evolving models of the immunopathogenesis of T cell-mediated drug allergy: The role of host, pathogens, and drug response

Immune-mediated (IM) adverse drug reactions (ADRs) are an underrecognized source of preventable morbidity, mortality, and cost. Increasingly, genetic variation in the HLA loci is associated with risk of severe reactions, highlighting the importance of T-cell immune responses in the mechanisms of both B cell-mediated and primary T cell-mediated IM-ADRs. In this review we summarize the role of host genetics, microbes, and drugs in IM-ADR development; expand on the existing models of IM-ADR pathogenesis to address multiple unexplained observations; discuss the implications of this work in clinical practice today; and describe future applications for preclinical drug toxicity screening, drug design, and development.

Progress in understanding the genomic basis for adverse drug reactions: a comprehensive review and focus on the role of ethnicity

A major goal of the field of pharmacogenomics is to identify the genomic causes of serious adverse drug reactions (ADRs). Increasingly, genome-wide association studies (GWAS) have been used to achieve this goal. In this article, we review recent progress in the identification of genetic variants associated with ADRs using GWAS and discuss emerging themes from these studies. We also compare aspects of GWAS for ADRs to GWAS for common diseases. In the second part of the article, we review progress in performing pharmacogenomic research in multi-ethnic populations and discuss the challenges and opportunities of investigating genetic causes of ADRs in ethnically diverse patient populations.

T cell-mediated hypersensitivity reactions to drugs

The immunological mechanisms driving delayed hypersensitivity reactions (HSRs) to drugs mediated by drug-reactive T lymphocytes are exemplified by several key examples and their human leukocyte antigen (HLA) associations: abacavir and HLA-B*57:01, carbamazepine and HLA-B*15:02, allo-purinol and HLA-B*58:01, and both amoxicillin-clavulanate and nevirapine with multiple class I and II alleles. For HLA-restricted drug HSRs, specific class I and/or II HLA alleles are necessary but not sufficient for tissue specificity and the clinical syndrome. Several models have been proposed to explain the immunopathogenesis of severe T cell-mediated drug HSRs, and our increased understanding of the risk factors and mechanisms involved in the development of these reactions will further the development of sensitive and specific strategies for preclinical screening that will lead to safer and more cost-effective drug design.