TAP1 and TAP2 polymorphisms associated with ankylosing spondylitis in genetically homogenous Chinese Han population

Association study of TAP and HLA-I gene combination with chronic hepatitis C virus infection in a Han population in China

Host immune system genes play key roles in the progression of chronic hepatitis C virus (HCV) infection. Transporters associated with antigen processing (TAP) play an important role in the loading of viral peptides onto MHC class I molecules. This study aimed to investigate the association between TAP gene polymorphisms and chronic HCV in a Chinese Han population. A total of 232 chronic hepatitis C (CHC) patients and 362 healthy individuals were recruited from the Han population in Yunnan province in southwest China, and a TaqMan SNP genotyping assay was used to detect six single nucleotide polymorphisms (SNPs) of TAP1 and three SNPs of TAP2 genes. The association of the TAP gene with CHC was analysed at the allele, genotype, and haplotype levels. There were no significant differences in the allele and genotype frequencies of these SNPs in the TAP gene between CHC patients and controls after Bonferroni correction. A novel TAP1 allele (TAP1*unknown_1: rs41555220-rs41549617-rs1057141-rs1135216-rs1057149-rs41551515: G-G-A-G-G-G) was only present in the CHC group, and this allele significantly increased susceptibility to CHC (p = .005, odds ratio [OR] = 11.105. 95% confidence interval [CI]: 1.362-90.558). Homozygous TAP1*03:01/TAP1*03:01 was observed only in the CHC group that exhibited an obvious risk for CHC (p = .002, OR = 9.637, 95% CI: 1.153-80.574). And the haplotype TAP1*unknown_1-TAP2*01:01 was only present in the CHC group and indicated a significant risk for CHC (p = .002, OR = 9.498, 95% CI: 1.140-79.149). We observed significant interactions among HLA-A, -B,C, TAP1, and TAP2 alleles, and combination analysis revealed that the combination of TAP1*01:01-TAP2*01:01-HLA-B*35:01 was only present in the control group (2.2%) and resulted in significantly increased resistance to CHC (p = .002, OR = 0.096, 95% CI: 0.012-0.759). Whereas, the combination of TAP1*01:01-TAP2*01:01-HLA-C*07:02 and TAP1*03:01-TAP2*01:01-HLA-C*01:02 increased the susceptibility to CHC significantly (p = .001, OR = 2.016, 95% CI: 1.309-3.106 and p = .002, OR = 8.070, 95% CI: 1.018-63.997, respectively). Our results indicated that TAP and HLA-I may exert a combined effect on CHC susceptibility in the Chinese Han population.

The association of TAP polymorphisms with non-small-cell lung cancer in the Han Chinese population

The host immune system plays a crucial role in multiple types of cancer, including non-small-cell lung cancer (NSCLC). Transporter associated with antigen processing (TAP) protein heterodimer complexes might promote intracellular antigen peptide binding with class I major histocompatibility complex (MHC-I) molecules, and in recent years, TAP1 and TAP2 have been reported to be associated with multiple cancer risks. In the current study, we investigated the association of single-nucleotide polymorphisms (SNPs) in TAP1 and TAP2 with NSCLC in a Han Chinese population. Six and seven TAP1 and TAP2 SNPs, respectively, were genotyped and analysed in healthy controls and NSCLC patients. Based on our data, none of the six SNPs in TAP1 is associated with NSCLC risk (P > 0.0038). However, rs2228396 alleles in TAP2 were significantly different between NSCLC patients and healthy controls, and the A allele might be associated with an increased risk of this cancer (P = 0.001, OR = 1.65, 95%CI: 1.23 ∼ 2.21). Moreover, the genotype frequencies of rs2228396 were significantly different between patients and healthy controls (P = 7 × 10^-4). Additionally, TAP2 rs241441 alleles exhibited a trend of difference between NSCLC patients and healthy controls, with the C allele possibly being associated with increased risk of NSCLC (P = 0.013; OR = 1.30, 95%CI: 1.06 ∼ 1.60). Moreover, the genotypes of rs241441 in TAP2 showed a significant difference between NSCLC patients and healthy controls (P = 1 × 10^-4). In haplotype analysis, the TAP2 SNP haplotype (CAC, TAP2*0102) was significantly associated with increased NSCLC risk in the Han Chinese population (P = 0.003; OR = 1.57, 95%CI: 1.17 ∼ 2.10). Our results indicate that TAP2 SNPs (rs2228396 and rs241441) have a potential role in NSCLC pathogenesis.

Polymorphisms in transporter associated with antigen presenting are associated with cervical intraepithelial neoplasia and cervical cancer in a Chinese Han population

The host immune system plays an important role in infectious diseases and cancers. The heterodimer formed by transporter associated with antigen presenting (TAP)1 and TAP2 is responsible for intracellular peptide loading onto MHC-I molecules. Studies have shown that single-nucleotide polymorphisms (SNPs) in TAP genes might affect the expression and function of TAP and be associated with cancer risk. We aimed to investigate the association of SNPs in the TAP1 and TAP2 genes with cervical intraepithelial neoplasia (CIN) and cervical cancer (CC) in a Chinese Han population. Six SNPs in the TAP1 gene and seven in the TAP2 gene were selected. The 13 SNPs were genotyped in 1255 healthy individuals, 575 patients with CIN and 1034 patients with CC using the SNaPshot assay. The association between these SNPs and CIN and CC risk was analysed. The allelic and genotypic distributions of rs41549617 and rs1135216 showed significant differences between the control and CC groups (P < 0.0038). The T allele of rs41549617 was associated with a decreased risk of CC (OR = 0.476, 95%CI: 0.286-0.791). Moreover, the G allele of rs1135216 appears to be associated with a decreased risk of CC (OR = 0.746; 95%CI: 0.632-0.881). The allele and genotype distribution of rs241441 showed a significant difference between the control and CC groups (P < 0.0038), and the rs241441 G allele was associated with an increased risk of CC (OR = 1.232, 95%CI: 1.092-1.398). In addition, the results of the association between TAP alleles and CC showed that TAP1*020101 and TAP1*0301 have an association with CC (P = 0.001 and P = 0.002, respectively). Our results demonstrate that the TAP1 and TAP2 genes are associated with CC in the Chinese Han population.

Polymorphisms in Processing and Antigen Presentation-Related Genes and Their Association with Host Susceptibility to Influenza A/H1N1 2009 Pandemic in a Mexican Mestizo Population

(1) Background: The influenza A/H1N1 pdm09 virus rapidly spread throughout the world. Despite the inflammatory and virus-degradation pathways described in the pathogenesis of influenza A virus (IAV) infection, little is known about the role of the single nucleotide polymorphisms (SNPs) in the genes involved in the processing and antigenic presentation-related mechanisms. (2) Methods: In this case-control study, we evaluated 17 SNPs in five genes (TAP1, TAP2, TAPBP, PSMB8, and PSMB9). One hundred and twenty-eight patients with influenza A/H1N1 infection (INF-P) and 111 healthy contacts (HC) were included; all of them are Mexican mestizo. (3) Results: In allele and genotype comparison, the rs241433/C allele (TAP2), as well as AG haplotype (rs3763365 and rs4148882), are associated with reduced risk for influenza A/H1N1 infection (p < 0.05). On the other hand, the rs2071888G allele (TAPBP) and GG haplotype (rs3763365 and rs9276810) are associated with a higher risk for influenza A/H1N1 infection. In addition, after adjustment for covariates, the association to a reduced risk for influenza A/H1N1 infection remains with rs241433/C allele (p < 0.0001, OR = 0.24, 95% CI = 0.13-0.43), and the association with TAPBP is also maintained with the G allele (p = 0.0095, OR = 1.89, 95% CI = 1.17-3.06) and GG genotype models (p < 0.05, OR = 2.18, 95% CI = 1.27-3.74). (4) Conclusion: The rs241433/C allele and AC genotype (TAP2) and the AG haplotype are associated with a reduced risk for influenza A/H1N1 infection. In addition, the rs2071888/G allele and GG genotype (TAPBP) and the GG haplotype are associated with a higher risk for developing influenza A/H1N1 infection in a Mexican mestizo population.

Analysis of transporter associated with antigen presentation (TAP) genes polymorphisms with HIV-1 infection

Human leukocyte antigen (HLA) class I molecules of the human major histocompatibility complex (MHC) play an important role in modulating immune response. HLA class I molecules present antigenic peptides to CD8⁺ T cells and thereby play a role in the immune surveillance of cells infected with viruses. TAP1 and TAP2 are MHC-II-encoded genes necessary for the generation of a cellular immune response and polymorphism of these genes can influence the specificity of peptides preferentially presented by the MHC class I molecules and the outcome of the immune response. Several studies implicated genetic variation in TAP genes to various immune-mediated and infectious diseases. To determine the correlation between HIV-1 infection and the TAP1 and TAP2 genes polymorphisms, we performed PCR–RFLP assay of these genes in 500 HIV-1 seropositives and the matched seronegative individuals. Statistical analysis of the data disclosed no correlation between TAP1 (C/T intron 7) gene polymorphism and HIV-1/AIDS disease. However, the current results demonstrated that the heterozygous A/G [OR (95% CI) 1.39 (1.06–1.83), P = 0.0171] and homozygous G/G [OR (95% CI) 3.38(1.56–7.46), P = 0.0010] variants of TAP2 (A/G exon 11) (T665A) gene are positively associated with an increased risk of HIV-1/AIDS infection. This case–control analysis might suggest a possible role of TAP2 (A/G exon 11) (T665A) gene in the susceptibility to HIV-1 infection and disease outcome among North Indian patients.

An update meta-analysis and systematic review of TAP polymorphisms as potential biomarkers for judging cancer risk

OBJECTIVE

Transporter associated with antigen processing protein (TAP) is a heterodimer protein consist of TAP1 and TAP2, act a pivotal part in the immune surveillance. In recent days, controversial relationships were reported between TAP polymorphisms and cancer risk, thus, a systematic meta-analysis was performed to resolve this discrepancy.

METHODS

We searched the PubMed, EMbase, Web of Science, CNKI and Wanfang databases, the cited references were also manually searched again, covering all the papers published until March 25, 2018. Quality assessment was conducted using the Newcastle-Ottawa Scale. All the meta-analysis was conducted with Stata version 12.0 software to assess the strength of the association.

RESULTS

4719 cases and 4215 controls from 24 case-control studies related to TAP polymorphisms were enrolled. There was no significant association between TAP1-rs1135216, TAP1-rs4148873, TAP2-rs2228396, TAP2-rs241447 and TAP2-rs4148873 and cancer sensibility. Interestingly, a significant positive association was observed between TAP2 rs4148876 C/T polymorphism and increase cancer risk in homozygote and recessive models. Further in-silico results indicated the expression of TAP2 in cancer tissue is higher than that in normal tissue (cervical cancer, TPM = 70.2 vs. 24.0 respectively, P <  0.01; acute myeloid leukemia, TPM = 52.5 vs. 8.8 respectively, P <  0.01), and influence the survival time of acute myeloid leukemia patients (Log-rank P <  0.05).

CONCLUSIONS

Our finding suggested that TAP1-rs1135216, TAP1-rs4148873, TAP2-rs2228396, TAP2-rs241447 and TAP2-rs4148873 might not be involved in cancer risk, but the T allele of TAP2-rs4148876 might be a potential biomarker for judging cancer risk, and larger-scale studies are required to confirm our findings.

Genetic association between TAP1 and TAP2 polymorphisms and ankylosing spondylitis: a systematic review and meta-analysis

OBJECTIVES

Ankylosing spondylitis (AS) is a chronic inflammatory joint disease. The transporter associated with antigen processing (TAP) has been identified to play an important role in immune response as well as the HLA-associated diseases. The aim of our meta-analysis was to investigate the contribution of TAP (TAP1 and TAP2) polymorphisms to the risk of AS.

METHODS

Meta-analyses were performed between 2 polymorphisms in TAP1 (TAP1-333, -637) and 3 polymorphisms in TAP2 (TAP2-379, -565, and -665) and AS.

RESULTS

The meta-analyses were involved with 6 studies with 415 cases and 659 controls. Significant association was found between TAP1-333Val, TAP1-637Gly, and TAP2-565Thr and AS compared with combined control group (TAP1-333Val: p = 0.009, OR = 1.40, 95% CI 1.09-1.80; TAP1-637Gly: p = 0.002, OR = 1.48, 95% CI 1.15-1.91; p = 0.03, OR = 1.38, 95% CI 1.04-1.84). Subgroup analysis shown that significant association was only found in AS when compared with HLA-B27-negative controls (TAP1-333Val: p = 0.004, OR = 1.53, 95% CI 1.14-2.06; TAP1-637Gly: p = 0.004, OR = 1.52, 95% CI 1.15-2.02; p = 0.02, OR = 1.56, 95% CI 1.09-2.24), but not in AS when compared with HLA-B27-positive controls (p > 0.05). Moreover, no significant associations were found between haplotypes in TAP1 and TAP2 in both the combined and the subgroup analyses (p > 0.05).

CONCLUSIONS

TAP1-333Val, TAP1-637Gly, and TAP2-565Thr were likely to be associated with AS.

Biophysical Approaches Facilitate Computational Drug Discovery for ATP-Binding Cassette Proteins

Although membrane proteins represent most therapeutically relevant drug targets, the availability of atomic resolution structures for this class of proteins has been limited. Structural characterization has been hampered by the biophysical nature of these polytopic transporters, receptors, and channels, and recent innovations to in vitro techniques aim to mitigate these challenges. One such class of membrane proteins, the ATP-binding cassette (ABC) superfamily, are broadly expressed throughout the human body, required for normal physiology and disease-causing when mutated, yet lacks sufficient structural representation in the Protein Data Bank. However, recent improvements to biophysical techniques (e.g., cryo-electron microscopy) have allowed for previously “hard-to-study” ABC proteins to be characterized at high resolution, providing insight into molecular mechanisms-of-action as well as revealing novel druggable sites for therapy design. These new advances provide ample opportunity for computational methods (e.g., virtual screening, molecular dynamics simulations, and structure-based drug design) to catalyze the discovery of novel small molecule therapeutics that can be easily translated from computer to bench and subsequently to the patient's bedside. In this review, we explore the utility of recent advances in biophysical methods coupled with well-established in silico techniques towards drug development for diseases caused by dysfunctional ABC proteins.

Mutations in the B30.2 domain of pyrin and the risk of ankylosing spondylitis in the Chinese Han population: a case-control study

Ankylosing spondylitis (AS) and familial Mediterranean fever (FMF) are a common autoimmune disease and a classic autoinflammatory disease, respectively. Mediterranean fever (MEFV) encodes the pyrin protein and is the causal disease gene in FMF. This protein is an important regulator of innate immunity and may play a key role in the development of AS. To identify the mutations in the B30.2 domain of pyrin and to uncover the relationships between these mutations and AS risk in the Chinese Han population, we extracted genomic DNA from the peripheral blood of 200 AS patients and 200 matched controls and performed polymerase chain reactions (PCRs) and direct sequencing on those samples. Statistical analysis indicated that only Met694Val (rs61752717) in the B30.2 domain of pyrin could affect the risk of AS (P = 0.042; odds ratio [OR] = 5.103; 95% confidence interval [CI] = 1.111-23.437 for the model of Met (M) vs. Val (V), P = 0.040; OR = 5.211; 95% CI = 1.127-24.091 for the model of MM vs. MV+VV). Moreover, M694V is significantly associated with a higher level of erythrocyte sedimentation rate (ESR) and C-reactive protein (CRP) in AS patients. Our results are the first to suggest that the M694V allele of the pyrin was associated with AS risk in the Chinese Han population and that this mutation may be associated with the inflammatory response in the development of AS.

Genomic, Transcriptomic, and Lipidomic Profiling Highlights the Role of Inflammation in Individuals With Low High-density Lipoprotein Cholesterol

Objective—

Low high-density lipoprotein cholesterol (HDL-C) is associated with cardiometabolic pathologies. In this study, we investigate the biological pathways and individual genes behind low HDL-C by integrating results from 3 high-throughput data sources: adipose tissue transcriptomics, HDL lipidomics, and dense marker genotypes from Finnish individuals with low or high HDL-C (n=450).

Approach and Results—

In the pathway analysis of genetic data, we demonstrate that genetic variants within inflammatory pathways were enriched among low HDL-C associated single-nucleotide polymorphisms, and the expression of these pathways upregulated in the adipose tissue of low HDL-C subjects. The lipidomic analysis highlighted the change in HDL particle quality toward putatively more inflammatory and less vasoprotective state in subjects with low HDL-C, as evidenced by their decreased antioxidative plasmalogen contents. We show that the focal point of these inflammatory pathways seems to be the HLA region with its low HDL-associated alleles also associating with more abundant local transcript levels in adipose tissue, increased plasma vascular cell adhesion molecule 1 (VCAM1) levels, and decreased HDL particle plasmalogen contents, markers of adipose tissue inflammation, vascular inflammation, and HDL antioxidative potential, respectively. In a population-based look-up of the inflammatory pathway single-nucleotide polymorphisms in a large Finnish cohorts (n=11 211), no association of the HLA region was detected for HDL-C as quantitative trait, but with extreme HDL-C phenotypes, implying the presence of low or high HDL genes in addition to the population-genomewide association studies–identified HDL genes.

Conclusions—

Our study highlights the role of inflammation with a genetic component in subjects with low HDL-C and identifies novel cis -expression quantitative trait loci ( cis -eQTL) variants in HLA region to be associated with low HDL-C.

Genetic evidence of TAP1 gene variant as a susceptibility factor in Indian leprosy patients

The heterodimeric transporter associated with antigen processing (TAP) gene loci is known to play a vital role in immune surveillance. We investigated a possible association of gene polymorphisms both in TAP1 and TAP2 in a cohort of clinically classified leprosy patients (n=222) and in ethnically matched controls (n=223). The TAP1 and TAP2 genes were genotyped for four single nucleotide polymorphisms TAP1 (rs1057141 Iso333Val and rs1135216 Asp637Gly) and TAP2 (rs2228396 Ala565Thr and rs241447 Ala665Thr) by direct sequencing and ARMS-PCR. The minor allele of TAP1 637G contributes to an increased risk to leprosy compared to controls (OR: 1.68, 95% CI 1.2-2.36, P=0.0057). An increased risk for the variant minor allele of the TAP1 637G to multibacillary (BL+LL) or paucibacillary (BT+TT) infections was also observed [multibacillary vs. controls (OR: 1.56, 95% CI 1.07-2.28, P=0.054); paucibacillary vs. controls (OR: 1.92, 95% CI 1.21-3.01, P=0.013)]. In the dominant model, the genotypes of the TAP1 rs1135216AG+GG additionally contributed to an increased risk. Overall our findings demonstrate that the TAP1 gene variant (rs1135216 Asp637Gly) influences the susceptibility to clinically classified leprosy patients in Indian population.

Genetic polymorphisms inside and outside the MHC improve prediction of AS radiographic severity in addition to clinical variables

OBJECTIVE

The aim of this study was to analyse if single nucleotide polymorphisms (SNPs) inside and outside the MHC region might improve the prediction of radiographic severity in AS.

METHODS

A cross-sectional multi-centre study was performed including 473 Spanish AS patients previously diagnosed with AS following the Modified New York Criteria and with at least 10 years of follow-up from the first symptoms of AS. Clinical variables and 384 SNPs were analysed to predict radiographic severity [BASRI-total (BASRI-t) corrected for the duration of AS since first symptoms] using multivariate forward logistic regression. Predictive power was measured by the area under the receiver operating characteristic curve (AUC), specificity, sensitivity, positive predictive value (PPV) and negative predictive value (NPV).

RESULTS

The model with the best fit measured radiographic severity as the BASRI-t 60th percentile and combined eight variables: male gender, older age at disease onset and six SNPs at ADRB1 (rs1801253), NELL1 (rs8176785) and MHC (rs1634747, rs9270986, rs7451962 and rs241453) genes. The model predictive power was defined by AUC = 0.76 (95% CI 0.71, 0.80), being significantly better than the model with only clinical variables, AUC = 0.68 (95% CI 0.63, 0.73), P = 0.0004. Internal split-sample analysis proved the validation of the model. Patient genotype for SNPs outside the MHC region, inside the MHC region and clinical variables account for 26, 38 and 36%, respectively, of the explained variability on radiographic severity prediction.

CONCLUSION

Prediction of radiographic severity in AS based on clinical variables can be significantly improved by including SNPs both inside and outside the MHC region.

Radiographic severity of ankylosing spondylitis is associated with polymorphism of the large multifunctional peptidase 2 gene in the Spondyloarthritis Research Consortium of Canada cohort

OBJECTIVE

There are limited data on genetic predictors of radiographic progression. The aim of this study was to examine polymorphisms in genes involved in antigen presentation and their effect on radiographic severity and progression.

METHODS

Caucasian patients with ankylosing spondylitis (AS) (diagnosed according to the modified New York criteria) from 2 Canadian centers were enrolled. Patients in the progression part of the study had at least 2 sets of radiographs obtained at a minimum gap of 1.5 years, with a modified Stoke Ankylosing Spondylitis Spine Score (mSASSS). Peripheral blood DNA was used for genotyping a panel of 13 coding-region single-nucleotide polymorphisms (SNPs) in ERAP1, LMP2, LMP7, TAP1, and TAP2. Linear regression analysis was performed to identify the predictors of the baseline mSASSS and logistic regression for predictors of progression. Progression was defined as an increase of 1 mSASSS unit per year.

RESULTS

A total of 241 AS patients (81% males; 82% HLA-B27-positive) were enrolled from the 2 centers for analysis of the predictors of baseline radiographic severity. In univariate analyses, the baseline mSASSS was associated with sex, disease duration, and SNPs rs30187 (ERAP1) and rs17587 (LMP2). In multivariate analyses, duration of disease (B = 0.74; P = 1 × 10(-11) ), sex (B = 12.1; P = 5 × 10(-5) ), and the LMP2 SNP rs17587 (B = 6.2; P = 0.01) were significantly associated with the baseline mSASSS. In multivariate analyses of progression, only the baseline mSASSS was a significant predictor (B = 0.03; P = 0.003).

CONCLUSION

This is the first study to demonstrate that LMP2 variants can affect radiographic severity in AS. The baseline mSASSS remains the strongest predictor of radiographic progression but explains only a fraction of the variability seen.

Association of TAP 1 and 2 gene polymorphisms with human immunodeficiency virus-tuberculosis co-infection

Major histocompatibility complex (MHC) class I binding peptides are carried from cytosol to the lumen of the endoplasmic reticulum (ER) by transporter associated with antigen processing (TAP), an integral ER membrane protein composed of two subunits, TAP1 and TAP2. Polymorphism in TAP genes may influence these proteins further affecting the antigen peptide presentation, indirectly resulting in the viral escape mechanism from cell-mediated immunity in human immunodeficiency virus (HIV). Our aim was to study the influence of these polymorphism in study groups with HIV-tuberculosis (TB) (n = 110), TB (n = 105), and HIV (n = 130) compared with healthy controls (n = 183), using the tetraprimer amplification refractory mutation system (ARMS)-polymerase chain reaction method. Our results demonstrated that the GG genotype at TAP1 position 333 and GA genotype at TAP1 position 637 were positively associated with HIV-TB co-infection and these genotypes may act as a risk factor for developing TB co-infection in HIV-positive individuals.