Relationship of HLA-DRB1 gene polymorphism with susceptibility to pulmonary tuberculosis: updated meta-analysis

HLA-SPREAD: a natural language processing based resource for curating HLA association from PubMed abstracts

Extreme complexity in the Human Leukocyte Antigens (HLA) system and its nomenclature makes it difficult to interpret and integrate relevant information for HLA associations with diseases, Adverse Drug Reactions (ADR) and Transplantation. PubMed search displays ~ 146,000 studies on HLA reported from diverse locations. Currently, IPD-IMGT/HLA (Robinson et al., Nucleic Acids Research 48:D948-D955, 2019) database houses data on 28,320 HLA alleles. We developed an automated pipeline with a unified graphical user interface HLA-SPREAD that provides a structured information on SNPs, Populations, REsources, ADRs and Diseases information. Information on HLA was extracted from ~ 28 million PubMed abstracts extracted using Natural Language Processing (NLP). Python scripts were used to mine and curate information on diseases, filter false positives and categorize to 24 tree hierarchical groups and named Entity Recognition (NER) algorithms followed by semantic analysis to infer HLA association(s). This resource from 109 countries and 40 ethnic groups provides interesting insights on: markers associated with allelic/haplotypic association in autoimmune, cancer, viral and skin diseases, transplantation outcome and ADRs for hypersensitivity. Summary information on clinically relevant biomarkers related to HLA disease associations with mapped susceptible/risk alleles are readily retrievable from HLASPREAD. The resource is available at URL http://hla-spread.igib.res.in/ . This resource is first of its kind that can help uncover novel patterns in HLA gene-disease associations.

Distribution of HLA-DRB1 alleles in BRICS countries with a high tuberculosis burden: a systematic review and meta-analysis

INTRODUCTION

Tuberculosis (TB) is the leading cause of death worldwide caused by a single infectious disease agent. Brazil, Russia, India, China, and South Africa (BRICS) account for more than half of the world's TB cases. Bacillus Calmette-Guérin (BCG) remains the only vaccine available despite its variable efficacy. Promising antigen-based vaccines have been proposed as prophylactic and/or immunotherapeutic approaches to boost BCG vaccination. Relevant antigens must interact with the range of human leukocyte antigen (HLA) molecules present in target populations; yet this information is currently not available.

METHODS

MEDLINE and EMBASE were systematically searched for articles published during 2013-2020 to measure the allelic frequencies of HLA-DRB1 in the BRICS.

RESULTS

In total, 67 articles involving 3,207,861 healthy individuals were included in the meta-analysis. HLA-DRB1 alleles *03, *04, *07, *11, *13, and *15 were consistently identified at high frequencies across the BRICS, with a combined estimated frequency varying from 52% to 80%. HLA-DRB1 alleles *01, *08, *09, *10, *12, and *14 were found to be relevant in only one or two BRICS populations.

CONCLUSIONS

By combining these alleles, it is possible to ensure at least 80% coverage throughout the BRICS populations.

The complex pattern of genetic associations of leprosy with HLA class I and class II alleles can be reduced to four amino acid positions

Leprosy is a chronic disease caused by Mycobacterium leprae. Worldwide, more than 200,000 new patients are affected by leprosy annually, making it the second most common mycobacterial disease after tuberculosis. The MHC/HLA region has been consistently identified as carrying major leprosy susceptibility variants in different populations at times with inconsistent results. To establish the unambiguous molecular identity of classical HLA class I and class II leprosy susceptibility factors, we applied next-generation sequencing to genotype with high-resolution 11 HLA class I and class II genes in 1,155 individuals from a Vietnamese leprosy case-control sample. HLA alleles belonging to an extended haplotype from HLA-A to HLA-DPB1 were associated with risk to leprosy. This susceptibility signal could be reduced to the HLA-DRB1*10:01~ HLA-DQA1*01:05 alleles which were in complete linkage disequilibrium (LD). In addition, haplotypes containing HLA-DRB3~ HLA-DRB1*12:02 and HLA-C*07:06~ HLA-B*44:03~ HLA-DRB1*07:01 alleles were found as two independent protective factors for leprosy. Moreover, we replicated the previously associated HLA-DRB1*15:01 as leprosy risk factor and HLA-DRB1*04:05~HLA-DQA1*03:03 as protective alleles. When we narrowed the analysis to the single amino acid level, we found that the associations of the HLA alleles were largely captured by four independent amino acids at HLA-DRβ1 positions 57 (D) and 13 (F), HLA-B position 63 (E) and HLA-A position 19 (K). Hence, analyses at the amino acid level circumvented the ambiguity caused by strong LD of leprosy susceptibility HLA alleles and identified four distinct leprosy susceptibility factors.

Despite global efforts to eliminate leprosy over the past 25 years, more than 200,000 new cases are reported annually, and leprosy still represents a major public health problem in endemic regions. Leprosy presents a strong link with the host genetic background. The most significant susceptibility factors are located in the MHC region and likely involve classical HLA genes. However, the molecular identity of the HLA class I/II-leprosy risk factor(s) has been a matter of longstanding scientific dispute. By conducting a comprehensive sequenced-based analysis of HLA class I and class II genes, we are able to provide a unifying view of the complex relationship of leprosy susceptibility and HLA alleles. In addition, we show that four amino acid polymorphisms in HLA-DRβ1, HLA-B and HLA-A are sufficient to explain the majority of leprosy-HLA associations which opens the way for select protein-HLA peptide binding studies.

Frequent transfusion and specific HLA-DRB1 alleles correlate independently with Miltenberger blood group alloimmunization in dialysis patients

Anti-"Mi^a " is the most frequent irregular RBC antibody in Taiwan due to high prevalence of Miltenberger antigens. Dialysis patients, a special patient group that needs frequent transfusions of RBCs, may have the greatest risk for developing anti-"Mi^a " antibodies. The aim of this study was to investigate the association between specific HLA-DRB1 alleles and Mi alloimmunization among dialysis patients. A cohort of 267 maintenance dialysis patients who had ever received at least one RBCs transfusion was enrolled. Anti-"Mi^a " was identified in patients' serum using the manual polybrene technique and HLA-DRB1 genotyping was carried out using polymerase chain reaction and sequence-specific oligonucleotide probe nonradioactive hybridization. Twenty-one (7.9%) of patients had positive anti-"Mi^a " tests and had received significantly more units of RBC transfusions than those without anti-"Mi^a " antibodies (11.3 ± 14.5 U vs 4.5 ± 10.1 U, P = .005). DRB1*04, *07, and *09 alleles were also more prevalent in patients with anti-"Mi^a " compared to those without Mi III alloimmunization. The multivariate logistic regression analysis showed that the number of RBC transfusions and the presence of DRB1*04, *07, and *09 phenotypes correlated independently with Mi III immunization (Odds ratios [OR] 1.05 (P = .001) for each unit of RBCs transfused; ORs 4.80 (P = .006), 12.29 (P = .005), and 5.42 (P = .003) for presence of DRB1*04, *07, and *09, respectively). This study is the first to demonstrate markedly high prevalence of Mi III alloimmunization in dialysis patients of Taiwan. Extending Mi III matching for RBC transfusions in susceptible dialysis patients may help to reduce the risk of Mi III alloimmunization in this patient population.

An HLA class II locus, previously identified by a genome-wide association study, is also associated with susceptibility to pulmonary tuberculosis in a Chinese population

OBJECTIVE

Genome-wide association study (GWAS) in Icelanders identified HLA class II sequence variants on chromosome 6p21 as tuberculosis (TB) susceptibility loci. To evaluate the role of these loci in other populations with different ancestry, we conducted a case-control study in Chinese population.

METHODS

We genotyped two genetic variants (rs9272461 and rs9271300) on the reported chromosome 6p21 in 739 pulmonary tuberculosis (PTB) cases and 749 healthy controls from Chinese Han population using TaqMan allelic discrimination assay. Logistic regression was applied to evaluate the association between genetic variants and PTB risk and to estimate corresponding odds ratios (ORs) and 95% confidence intervals (95%CIs).

RESULTS

We found that rs9272461 was significantly associated with the risk of PTB in various genetic models (dominant OR = 0.75, 95%CI: 0.61-0.92; recessive OR = 0.64, 95%CI: 0.46-0.90, and additive OR = 0.78, 95%CI: 0.67-0.90). Moreover, in the stratified analysis in additive model, the association was also significant in the old (age ≥ 48 years) (OR = 0.76, 95%CI: 0.62-0.93; P = .008), men (OR = 0.71, 95%CI: 0.59-0.85; P < .001), and new PTB cases (OR = 0.76, 95%CI: 0.65-0.90; P = .001). The association results were similar between the microbiologically negative (OR = 0.78, 95%CI: 0.64-0.94; P = .008) and positive cases (OR = 0.77, 95%CI: 0.64-0.93; P = .008). We did not observe significant association for rs9271300 neither in the overall analysis (additive model: OR = 0.98, 95%CI: 0.85-1.13; P = .776) nor in the stratified analysis.

CONCLUSIONS

Our findings indicate that the HLA class II locus also affects the susceptibility to PTB in Chinese population. Further validation studies and function experiments are required to confirm the roles of the discovered variant.

The role of human host genetics in tuberculosis resistance

INTRODUCTION

Tuberculosis (TB) remains a public health problem: the latest estimate of new incident cases per year is a staggering 10.4 million. Despite this overwhelming number, the majority of the immunocompetent population can control infection with Mycobacterium tuberculosis. The human genome underlies the immune response and contributes to the outcome of TB infection. Areas covered: Investigations of TB resistance in the general population have closely mirrored those of other infectious diseases and initially involved epidemiological observations. Linkage and association studies, including studies of VDR, SLC11A1 and HLA-DRB1 followed. Genome-wide association studies of common variants, not necessarily sufficient for disease, became possible after technological advancements. Other approaches involved the identification of those individuals with rare disease-causing mutations that strongly predispose to TB, epistasis and the role of ethnicity in disease. Despite these efforts, infection outcome, on an individual basis, cannot yet be predicted. Expert commentary: The early identification of future disease progressors is necessary to stem the TB epidemic. Human genetics may contribute to this endeavour and could in future suggest pathways to target for disease prevention. This will however require concerted efforts to establish large, well-phenotyped cohorts from different ethnicities, improved genomic resources and a better understanding of the human genome architecture.

The Role of Host Genetics (and Genomics) in Tuberculosis

Familial risk of tuberculosis (TB) has been recognized for centuries. Largely through studies of mono- and dizygotic twin concordance rates, studies of families with Mendelian susceptibility to mycobacterial disease, and candidate gene studies performed in the 20th century, it was recognized that susceptibility to TB disease has a substantial host genetic component. Limitations in candidate gene studies and early linkage studies made the robust identification of specific loci associated with disease challenging, and few loci have been convincingly associated across multiple populations. Genome-wide and transcriptome-wide association studies, based on microarray (commonly known as genechip) technologies, conducted in the past decade have helped shed some light on pathogenesis but only a handful of new pathways have been identified. This apparent paradox, of high heritability but few replicable associations, has spurred a new wave of collaborative global studies. This review aims to comprehensively review the heritability of TB, critically review the host genetic and transcriptomic correlates of disease, and highlight current studies and future prospects in the study of host genomics in TB. An implicit goal of elucidating host genetic correlates of susceptibility to Mycobacterium tuberculosis infection or TB disease is to identify pathophysiological features amenable to translation to new preventive, diagnostic, or therapeutic interventions. The translation of genomic insights into new clinical tools is therefore also discussed.

The HLA-DRB1 allele polymorphisms and nasopharyngeal carcinoma

Human leukocyte antigen (HLA)-DRB1 has been reported to influence individual's susceptibility to nasopharyngeal carcinoma (NPC) by many studies in recent years; however, these studies provided controversial results. The meta-analysis was thus conducted here to estimate the relationship between HLA-DRB1 polymorphisms and NPC. After an extensive review of journals from various databases (PubMed, the Web of Science, Embase, China National Knowledge Internet (CNKI), and Wanfang Database), 8 out of 69 case-control studies, including 778 cases and 1148 controls, were extracted. The results showed that 4 of 13 polymorphisms allele are statistically significantly associated with NPC, among them, HLA-DRB1*3, HLA-DRB1*9, and HLA-DRB1*10 may increase the risk of NPC while HLA-DRB1*01 has the opposite effect. The pooled odds ratio and 95 % confidence interval (CI) were 1.702 [95 % CI (1.047, 2.765)], 1.363 [95 % CI (1.029, 1.806)], 1.989 [95 % CI (1.042, 3.799)], and 0.461 [95 % CI (0.315, 0.676)], respectively. In a further ethnicity-based subgroup analysis, HLA-DRB1*08, HLA-DRB1*11, and HLA-DRB1*16 were found to be linked with NPC in Asian, Tunisian, and Caucasian, respectively. In Asian, HLA-DRB1*03, 08, and 10 may elevate the risk whereas HLA-DRB1*09 could lower it. In Tunisian, HLA-DRB1*01 and 11 are the protective factors while HLA-DRB1*03 is the only risk factor. In Caucasian, HLA-DRB1*01 and 03 increase the risk and HLA-DRB1*16 lowers it. The most frequent statistically associated gene is found to be HLA-DRB1*03 which has protective influence on Asian and Tunisian. In conclusion, HLA-DRB1*01, DRB1*03, DRB1*09, and DRB1*10 are related with NPC susceptibility, and the association of HLA-DRB1*08, DRB1*11, and DRB1*16 with NPC risk are significantly different in different ethnicities.

Association Analysis of Interleukin-17 Gene Polymorphisms with the Risk Susceptibility to Tuberculosis

BACKGROUND

Recently, many institutions have investigated the associations of interleukin-17 (IL17) polymorphisms with tuberculosis (TB) susceptibility, while those results are inconsistent. The purpose of this meta-analysis is to comprehensively assess whether IL17A rs22275913, IL17F rs763780, and IL17A rs3748067 polymorphisms are correlated with TB risk.

METHODS

Electronic bibliographic databases were searched for case-control studies which potentially focused on the relationship between the aforementioned polymorphisms and TB risk on October 15th, 2015. Pooled odds ratios (OR) combined with 95 % confidence intervals (CI) were employed to assess the associations.

RESULTS

There was no significant association of IL-17A rs22275913 polymorphism with susceptibility to TB in Asians or Caucasians. For IL-17A rs3748067 polymorphism, significant associations were observed in Asian (T vs. C: OR 1.461, 95 % CI 1.158-1.844, P = 0.001; TT vs. CC: OR 1.871, 95 % CI 1.140-3.069, P = 0.013; TT/TC vs. CC: OR 1.392 95 % CI 1.062-1.825, P = 0.017; TT vs.

TC/CC

OR 1.820, 95 % CI 1.111-2.981, P = 0.017). For IL-17F rs763780, we detected the significant associations under allele contrast, heterozygote, dominant and recessive models (C vs. T: OR 1.571, 95 % CI 1.352-1.824, P = 0.000; CT vs. TT: OR 1.624, 95 % CI 1.346-1.958, P = 0.000; CT/TT vs. TT: OR 1.639, 95 % CI 1.381-1.946, P = 0.000, respectively). The corresponding results were also detected in Asian populations (C vs. T: OR 1.068, 95 % CI 1.380-1.875, P = 0.000; CT vs. TT: OR 1.689, 95 % CI 1.390-2.053, P = 0.000; CT/TT vs. TT: OR 1.695, 95 % CI 1.420-2.023, P = 0.000), while there were no significant associations in Caucasian.

CONCLUSION

IL-17F rs763780 allele C and IL-17A rs3748067 allele C may be involved in the susceptibility to TB in Asian populations. There were no significant associations between IL-17A rs22275913 polymorphism and risk of TB.

Major Histocompatibility Complex and Malaria: Focus on Plasmodium vivax Infection

The importance of host and parasite genetic factors in malaria resistance or susceptibility has been investigated since the middle of the last century. Nowadays, of all diseases that affect man, malaria still plays one of the highest levels of selective pressure on human genome. Susceptibility to malaria depends on exposure profile, epidemiological characteristics, and several components of the innate and adaptive immune system that influences the quality of the immune response generated during the Plasmodium lifecycle in the vertebrate host. But it is well known that the parasite's enormous capacity of genetic variation in conjunction with the host genetics polymorphism is also associated with a wide spectrum of susceptibility degrees to complicated or severe forms of the disease. In this scenario, variations in genes of the major histocompatibility complex (MHC) associated with host resistance or susceptibility to malaria have been identified and used as markers in host-pathogen interaction studies, mainly those evaluating the impact on the immune response, acquisition of resistance, or increased susceptibility to infection or vulnerability to disease. However, due to the intense selective pressure, number of cases, and mortality rates, the majority of the reported associations reported concerned Plasmodium falciparum malaria. Studies on the MHC polymorphism and its association with Plasmodium vivax, which is the most widespread Plasmodium and the most prevalent species outside the African continent, are less frequent but equally important. Despite punctual contributions, there are accumulated evidences of human genetic control in P. vivax infection and disease. Herein, we review the current knowledge in the field of MHC and derived molecules (HLA Class I, Class II, TNF-α, LTA, BAT1, and CTL4) regarding P. vivax malaria. We discuss particularly the results of P. vivax studies on HLA class I and II polymorphisms in relation to host susceptibility, naturally acquired immune response against specific antigens and the implication of this knowledge to overcome the parasite immune evasion. Finally, the potential impact of such polymorphisms on the development of vaccine candidate antigens against P. vivax will be studied.