Association between two tumour necrosis factor intronic polymorphisms and HLA alleles

The gene for tumour necrosis factor (TNF) lies at the telomeric end of the class III region of the major histocompatibility complex (MHC). Polymorphisms within this gene have been implicated in the genetic background of a large number of common human diseases. Recently two polymorphisms, TNF +489 and +691, have been described in the first intron of TNF (+489, G to A transition; +691, G deletion) and disease associations have been reported; however, the pattern of linkage disequilibrium with other MHC alleles has not been studied. We have therefore studied the association of TNF alleles with HLA‐DR, ‐DQ and ‐B alleles in 216 healthy individuals from the north of England. The frequencies of the uncommon alleles were 0.08 (+489A) and 0.05 (+691G^del). The +489A allele is associated with carriage of DRB1*1104, DQB1*0301, B18 and B35. The +691G^del allele is associated with carriage of DRB1*13 *11, DQB1*0301 and B44. Knowledge of the pattern of association, indicating probable linkage disequilibrium, between these TNF alleles may be useful in studies aimed at determining the role of this locus in the genetic background of the large number of diseases which show genetic associations with MHC haplotypes.     

HLA and tumour necrosis factor (TNF) polymorphisms in ocular Behçet's disease

The role of HLA-B*51 and other major histocompatibility complex (MHC) genes in Beh?et's disease (BD) remains unknown. We have performed HLA and tumour necrosis factor (TNF) polymorphism analysis in BD and evaluated their contribution to ocular disease. In this study, 102 patients and 115 controls of Middle Eastern descent were investigated by HLA and B*51 subtyping using novel primers, and by LT alpha NCo 1 and TNF 308 promoter polymorphism analysis. The frequency of the HLA-B*51 family of alleles was raised in patients compared to controls (66% vs. 15%, Pc=2.5x10(-12), OR=10.9). The odds ratio (OR) of this group of alleles for subgroups of patients was as follows: non-ocular patients 7.8, all ocular patients 12.6, blind patients >22. HLA-B*51 subtyping detected B*5101, 07, 08 and 09 alleles, with a similar frequency among patients and controls. HLA-Cw*1602 was associated with B*5108, but was not an independent risk factor for disease. The LT alpha (TNFB*2) allele was associated with HLA-B*51 among patients and the frequency of this allele was significantly higher among completely blind patients compared to both non-ocular patients (P=0.048, OR >3.6) and to healthy controls (P=0.022, OR >4.3). The rare TNF-2 polymorphism at the TNF -308 promoter position was associated with HLA-B*50 (not B*51), and was not associated with BD. Thus, in this population the HLA*B51 family of alleles is a strong risk factor for BD, and in particular the development of ocular disease. HLA-B*51 subtyping did not define new markers for BD. A primary role for TNF gne polymorphisms in BD was not identified, but co-expression of the TNFB*2 allele with HLA-B*51 may contribute to severity of ocular disease.     

Association and linkage of leprosy phenotypes with HLA class II and tumour necrosis factor genes

Previous analyses indicate major gene control of susceptibility to leprosy per se and the HLA class II region has been implicated in determining susceptibility and control of clinical phenotype. Segregation analysis using data from 76 Brazilian leprosy multi-case pedigrees (1166 individuals) supported a two locus model as the best fit: a recessive major gene and a recessive modifier gene(s) (single locus vs two locus model, P = 0.0007). Combined segregation and linkage analysis to the major locus, showed strong linkage to HLA class II (HLA-DQB1 P = 0.000002, HLA-DQA1 P = 0.000002, HLA-DRB1 P = 0.0000003) and tumour necrosis factor genes (TNF P = 0.00002, LTA P = 0.003). Extended transmission disequilibrium testing, using multiple affected family members, demonstrated that the common allele TNF*1 of the -308 promoter region polymorphism showed linkage and/or association with disease per se, at a high level of significance (P < 0.0001). Two locus transmission disequilibrium testing suggested susceptibility (TNF*1/LTA*2) and protective (TNF*2/LTA*2) haplotypes in the class iii region. Taken together the segregation and HLA analyses suggest the possibility of more than one susceptibility locus in the MHC.     

Association between tumour necrosis factor gene polymorphisms and the clinical types of patients with chronic hepatitis B virus infection

A PCR restriction fragment length polymorphism assay was used to analyse single-nucleotide polymorphisms in the tumour necrosis factor (TNF)-alpha and TNF-beta genes of 56 patients with chronic severe hepatitis B virus (HBV) infection, 71 patients who either had chronic mild HBV infection or who were asymptomatic carriers, and 90 healthy controls. The serum TNF-alpha concentrations in patients with chronic severe HBV infection were compared to those of 30 healthy controls by radioimmunoassay. The frequencies of the TNF1/2 genotype and the TNF2 allele were greater in patients with chronic severe HBV infection than in healthy controls (25% vs. 11.1%, p 0.015; 12.5% vs. 5.6%, p 0.036, respectively) and patients with chronic mild HBV infection and asymptomatic carriers (25% vs. 8.8%, p 0.011; 12.5% vs. 4.2%, p 0.015, respectively). Heterozygotes carrying the TNF2 allele had higher levels of serum TNF-alpha than homozygotes for the wild-type allele among all patients with chronic severe HBV infection (p <0.01). The genotype distribution and allele frequency of TNF-beta were similar for patients with chronic severe HBV infection and healthy controls, but the frequency of the TNF-beta*2/2 genotype in patients with chronic mild HBV infection and asymptomatic controls was lower than for healthy controls (9.9% vs. 22.4%, p 0.043) or patients with chronic severe HBV infection (9.9% vs. 26.8%, p 0.043), although this was not significant after correction for multiple testing. It was concluded that TNF-alpha gene polymorphisms may play an important role as a host factor in the progression of HBV infection.     

中国傈僳族和怒族群体人类白细胞抗原Ⅰ类基因区Alu插入多态性研究

目的 研究中国两个隔离群体(傈僳族和怒族)人类白细胞抗原(human leukocyte antigen,HLA)Ⅰ类基因区域内5个HLA-Alu插入多态性(AluMICB、AluTF、AluHJ、AluHG和AluHF)的分布特征.方法 应用聚合酶链反应技术对中国两个隔离群体傈僳族(107人)和怒族(104人)进行HLA-Alu多态性分型.结合HLA基因分型数据,分析这两个群体中HLA-Alu插入与HLA-A、HLA-B和HLA-C基因的关系.根据HLA-Alu频率计算各群体间遗传距离,构建系统进化树.结果 AluTF和AluHF插入的频率在这两个群体间的差异有统计学意义(P＜0.05),其余位点差异无统计学意义.HLA-Alu插入与HLA的关联程度在两个群体中有差异,如AluTF*2与HLA-B* 56:01均有关联,但在傈僳族中呈强关联(74.0％),在怒族中仅存在中等程度的关联(30.7％).傈僳族和怒族群体中,HLA-Alu插入与HLA基因的不同亚型具有关联,如AluHG*2与HLA-A* 02的不同亚型存在关联.系统进化树显示中国傈僳族和怒族与我国南方群体及泰国人群聚为一支.结论 不同群体中HLA-Alu插入与HLA不同等位基因的关联程度存在差异,这种差异性为研究HLA Ⅰ类基因多样性的产生和进化、祖先单倍型的形成以及该区域内连锁不平衡和重组提供了新的线索.     

Haplospecific polymorphism between HLA B and tumor necrosis factor.

Polymorphisms were sought between HLA B and tumor necrosis factor (TNF) using three genomic probes. Extensive polymorphism was detected within a panel of 50 cell lines including 37 homozygotes representing 21 different ancestral haplotypes (AH). Following Taq I digestion of genomic DNA, we observed three allelic patterns with probe X (R17A) and four with probe V (R9A). Seven different allelic patterns were found with probe Y (M20A) after Taq I + Rsa I digestion. Family studies showed that the Y, X, and V alleles were inherited and segregated with HLA haplotypes. A striking feature of the allelic patterns detected by these probes was that cells with the same AH had identical Y, X, and V alleles (i.e., the alleles were haplotypic). Of 15 different Y-X-V haplotypes observed, 11 were found to be specific for a particular AH (i.e., were haplospecific). Four were shared by more than one AH, but in these instances there were extensive similarities in other regions within the major histocompatibility complex (MHC), for example, the Japanese 46.2 (HLA Bw46-DRw8) and the Chinese 46.1 (Bw46-DR9) share all alleles between HLA C and C4 and differ only in class II, suggesting their relatively recent divergence by recombination between C4 and DR. Surprisingly, two insulin-dependent diabetes mellitus (IDDM)-resistant but race-specific AHs 52.1 (Bw52-DRB1*1502, Japanese) and 7.1 (B7-DRB1*1501, Caucasoid) carry the same Y-X-V haplotype, suggesting the possibility of localizing gene(s) relevant to IDDM. The present study confirms that MHC AHs have been conserved en bloc, including the region between HLA B and TNF.     

Association between chronic cutaneous lupus erythematosus and HLA class II alleles

CCLE, a disease entity at the benign end of the lupus spectrum, is characterized by marked photosensitivity and skin lesions in sun-exposed areas. The histopathology of lesions resembles hypersensitivity type IV reactions. We have asked whether an association between class II alleles and CCLE exists. RFLP analysis of HLA-DQA genes revealed a Taq I HLA-DQA1 allelic restriction fragment overrepresented in a group consisting of 26 patients as xompared to healthy control individuals. This result was corroborated by typing with oligonucleotide probes. The presence of the DQA1^*0102 allele in the patients' group led to a relative risk of 4.57, with a statistical significance of p < 0.05 after correction for 36 comparisons. Although not statistically significant, it is interesting that all patients possess in at least one of their HLA-DQA1 alleles a nucleotide sequence coding for the amino acid glutamine at position 34 of the DQ molecule. The expected frequency of these alleles in the control population amounts to 82%. The HLA-DRB1^*16 allele, which is found in linkage disequilibrium with the HLA-DQA1^*0102 allele, is also observed at an increased frequency in the patient's group, though the association was not significant after correction for the number of comparisons. However, no association of CCLE with alleles at the HLA-DPB1 locus was found. The association of CCLE with certain HLA class II alleles points to an involvement of HLA-DQ and/or -DR molecules in the pathogenesis of the disease. Alternatively, genetic loci in linkage disequilibrium may code for elements which contribute to the development of CCLE. In conclusion, a genetic marker for CCLE is mapped to the human HLA class II region telomeric of the HLA-DP locus.     

Association of hepatocellular carcinoma risk with polymorphisms in tumour necrosis factor alpha gene in a Chinese Han population

Hepatocellular carcinoma (HCC) is the third leading cause of cancer‐related death worldwide. Studies have shown that the tumour necrosis factor alpha (TNF‐α) plays an important role in the development of HCC; however, the association between genetic variations of TNF‐α and HCC is not yet fully understood. To evaluate the correlation of TNF‐α polymorphisms with HCC, we randomly selected 327 HCC patients and 432 healthy controls, all these subjects reported Han nationality. Genotyping of four TNF‐α SNPs (rs1799724, rs1800629, rs1799964 and rs1800610) was performed using the matrix‐assisted laser desorption ionization‐time of flight mass spectrometry (MALDI‐TOF‐MS) method. Distributions of rs1799964 genotypes and rs1800610 alleles were found to be significantly different between cases and controls (p = .011, p = .001). The recessive model of rs1799964 significantly increased HCC risk (p = .0015), while the dominant and over‐dominant models of rs1800610 significantly reduced HCC risk (p = .0096, p = .014). Haplotype analysis of the four TNF‐α SNPs revealed that the TGTA haplotype was associated with a reduced HCC risk (p = .0033, OR = 0.53), while the TGTG haplotype was associated with an increased HCC risk (p = .0032, OR = 9.69). These findings indicated that specific TNF‐α polymorphisms may be associated with the susceptibility to HCC.     

Recurrent miscarriage and variant alleles of mannose binding lectin, tumour necrosis factor and lymphotoxin alpha genes.

Variant alleles of the mannose binding lectin (MBL) gene are associated with increased susceptibility to infection and polymorphisms of tumour necrosis factor and lymphotoxin alpha genes (TNF, LTA) are associated with increased severity of infection. Studies have associated recurrent miscarriage with low serum mannose binding lectin concentrations and premature membrane rupture and preterm delivery with elevated maternal and fetal levels of TNF and the TNF (- 308) polymorphism. In this study the frequencies of variant MBL, TNF and LTA alleles in 76 Caucasian couples with idiopathic recurrent miscarriage were compared with those in 69 Caucasian control couples with no history of miscarriage and at least one previous live birth. A new assay based on hybridization to immobilized sequence-specific oligonucleotides (SSO) was used to rapidly detect nine MBL, two TNF and two LTA sequence variants. The assay genotyped all the structural and promoter MBL variants known to influence serum MBL concentrations. This assay was more reliable than restriction digestion or nested allele-specific PCR for the structural variants at codon 54 or 52, respectively. Reliability for codon 57 alleles was not assessed because of the low frequency in this population. The MBL haplotype frequencies in antenatal controls were similar to those reported in other control populations. The frequencies of structural variant MBL genes and of low, medium and high MBL level haplotypes were similar in the recurrent miscarriage and control couples. The TNF and LTA haplotype frequencies were similar in the recurrent miscarriage and control couples. In this carefully defined population no association has been found between recurrent miscarriage and variant alleles of the MBL, TNF or LTA genes.     

Relationship of polymorphisms located in tumor necrosis factor region and HLA loci among Croatians

Polymorphism of TNFa, TNFb, and TNFd microsatellites, linkage disequilibrium (LD) within TNF region as well as relationship of TNF microsatellites with alleles at HLA‐A, ‐B, and ‐DRB1 loci was investigated on a sample of 160 Croatians, previously typed for HLA‐A, ‐B, and ‐DRB1 loci. Analysis of the relationship of TNF alleles and HLA specificities revealed that very strong associations exist between TNFa2, TNFb3, and TNFd2 alleles and HLA‐A*01, ‐B*08, and ‐DRB1*03 specificities, therefore placing them in the 8.1 ancestral haplotype. Similar findings were observed for TNFa11, TNFb4, and TNFd4 alleles and HLA specificities, which are a part of the 7.1 ancestral haplotype. Finally, multiple associations with significant P‐values were also observed between TNFa10, TNFb4, and TNFd4 microsatellite alleles and HLA‐A*02, ‐B*18, ‐DRB1*11 specificities which form the 18.3 ancestral hapolotype. Am. J. Hum. Biol. 2009. © 2008 Wiley‐Liss, Inc.     

Association of tumor necrosis factor polymorphisms with asthma and serum total IgE

Tumor necrosis factors (TNF; TNFA and TNFB) are major pro-inflammatory cytokines that are thought to be important in the pathogenesis of asthma. However, the functions of genetic polymorphisms in these cytokines have not been thoroughly examined in the context of asthma pathology. In an effort to discover polymorphism(s) in genes whose variant(s) have been implicated in asthma phenotypes, we examined the genetic effects of TNF (TNFA and TNFB) polymorphisms on asthma and total serum IgE level. Seven common single-nucleotide polymorphisms (SNP) in TNF genes were genotyped in a Korean asthma cohort (asthmatics n=550, normal controls n=171). Six common haplotypes could be constructed in the TNF gene cluster due to very strong LD between TNFA and TNFB, located 13 kb apart on chromosome 6p21. One SNP (TNFA-308G>A) showed a significant association with the risk of asthma (P=0.0004). The frequency of TNFA-308A allele-containing genotype in asthmatics (9.8%) was much lower than that in normal controls (22.9%). The protective effects of this polymorphism on asthma were also evident in separated subgroups by atopic status (P=0.05 in non-atopic subjects and P=0.003 in atopic subjects). The most common haplotype of the TNF gene (TNF-ht1[GGTCCGG]) was associated with total serum IgE (immunoglobulin E) levels in asthma patients, especially in non-atopic patients (P=0.004). Genetic variants of TNF might be involved in development of asthma and total serum IgE level in bronchial asthma patients. The results of this study could be helpful to understand the function of important TNF genes in asthma and IgE production.     

Association between − 308 tumour necrosis factor promoter polymorphism and bronchial hyperreactivity in asthma

BACKGROUND: Tumour necrosis factor (TNF) is a pivotal cytokine in the inflammation underlying asthma. The TNF gene is located in the polymorphic HLA class 3 region on chromosome 6p. Several polymorphisms in this region have been described and associated with alteration of TNF secretion in vitro. OBJECTIVE: In this study we tested the hypothesis that two such polymorphisms, lymphotoxin alpha NcoI B*1 and -308 TNF2 may be components of the genetic predisposition to asthma. METHODS: Five hundred and fifty-six random individuals were studied, comprising approximately equal numbers of asthmatic subjects, with or without atopy, and a nonatopic nonasthmatic control group. In addition, 355 subjects (172 asthmatics) from 60 multiplex families were typed at the LTalpha NcoI locus. RESULTS: There was an association between allele two of the -308 TNF polymorphism and bronchial hyperreactivity (OR 2.12, 95% CI 1.04-4.32, P = 0.036). However, there was no association with LTalpha NcoI alleles. To determine whether this was influenced by linkage disequilibrium within the MHC, 91 subjects with bronchial hyperreactivity and 85 control subjects were typed for class 2 and 3 alleles. Following identification of the extended TNF2 haplotype, we found no independent association of these alleles with BHR. CONCLUSIONS: We conclude that the -308 TNF2 promoter polymorphism may form a component of the genetic predisposition to BHR in asthma.     

Association of TNF polymorphisms with sarcoidosis, its prognosis and tumour necrosis factor (TNF)-alpha levels in Asian Indians

Tumour necrosis factor (TNF)-alpha, an important proinflammatory cytokine, has been implicated in the pathogenesis of sarcoidosis, a multi-systemic granulomatous disorder of unknown aetiology. Here, we report for the first time the association of TNF haplotypes and genotypes with sarcoidosis and its prognosis in the Indian population. Five potentially functional promoter polymorphisms in the TNFA gene and a LTA_NcoI polymorphism (+252 position) of the LTA gene were genotyped in a clinically well-defined cohort of North-Indian patients with sarcoidosis (n = 96) and their regional controls (n = 155). Serum TNF-alpha (sTNF-alpha) and serum angiotensin converting enzyme (SACE) levels were measured and correlated with genotypes and haplotypes. The TNFA_-1031 and TNFA_-863 polymorphisms were identified as markers for disease onset (FET P = 0.006 and 0.042 for TNFA_-1031 and TNFA_-863, respectively). Additionally, the allele A of LTA_NcoI polymorphism was shown to be prevalent in the 'no treatment' group (FET P = 0.005), while the G allele was associated with frequent relapses on drug withdrawal (P = 0.057). Furthermore, the TNFA-308G>A and the TNFA-238G>A polymorphisms were found to influence sTNF-alpha (P = 0.054 and 0.0005, respectively) and SACE levels (P = 0.0017 and 0.056, respectively). The haplotype frequencies were significantly different in the patients and the controls (P = 0.0067). The haplotype GTCCGG was identified as the major risk/susceptibility haplotype (P = 0.003) and was associated with increased SACE levels in the patient population. In conclusion, our study suggests an association of TNF polymorphisms with sarcoidosis.     

MICB polymorphisms and haplotypes with MICA and HLA alleles in Koreans

Major histocompatibility complex (MHC) class I chain-related gene B (MICB) is located within the human MHC class I region. The location of MICB in the MHC region may imply the presence of linkage disequilibrium with polymorphic MICA and human leukocyte antigen (HLA) loci. MICB is also polymorphic; however, MICB polymorphisms have not been investigated in Koreans. Using sequence-based typing (SBT), we estimated the allelic frequencies of MICB and haplotypes with MICA, HLA-B, and HLA-DRB1 at high resolution in a population of 139 unrelated Korean individuals. Eight MICB alleles were identified. The most frequent allele was MICB*005:02/*010 (57.2%), followed by *002 (11.5%), *004 (8.3%), *005:03 (8.3%), and *008 (6.8%). The most common two-locus haplotypes were MICB*005:02/*010-MICA*010 (19.4%), MICB*005:02/*010-DRB1*15:01 (6.5%), and MICB*005:02/*010-B*15:01 (10.4%); the most common three-locus haplotypes were B*15:01-MICA*010-MICB*005:02/*010 (5.8%) and MICA*010-MICB*005:02/*010-DRB1*04:06 (10.4%); and the most common four-locus haplotype was B*15:01-MICA*010-MICB*005:02/*010-DRB1*04:06 (5.8%). This is the first study to provide information about MICB allele frequencies and haplotypes with HLA in Koreans. These study results should help understand mechanisms of disease association between the MICB locus and neighboring loci in Koreans.     

Association of tumor necrosis factor and human leukocyte antigen DRB1 alleles with Graves' ophthalmopathy

Tumor necrosis factor (TNF)-alpha plays a central role in the development of ophthalmopathy in patients with Graves' disease (GD). The aim of this study was to investigate the association of TNF promoter polymorphisms at positions -1031 (T-1031C), -863 (C-863A), -857 (C-857T), -308 (G-308A), and -238 (G-238A) with Graves' ophthalmopathy (GO). We studied the distribution of TNF and human leukocyte antigen (HLA) DRB1 alleles in 228 Polish white patients with GD, 106 of whom had ophthalmopathy (NOSPECS class > or = III) and 248 healthy subjects. TNF -308A and HLA-DRB1*03 alleles were significantly increased in patients with GD compared with healthy subjects. Stratification analysis revealed no independent association of -308A with GD when the DRB1*03 status was considered. Subdividing GD according to eye involvement revealed that the distribution of TNF promoter haplotypes differed significantly in patients with or without ophthalmopathy. The haplotype containing the -238A allele was absent in GO. The association of G-238A with GO was independent of DRB1 alleles. These results indicate that TNF G-308A is associated with susceptibility to GD (however, this association is not independent of HLA-DRB1*03) and that TNF G-238A is associated with the development of ophthalmopathy, suggesting that G-238A or a gene in linkage disequilibrium may be disease modifying in GD.