Restriction fragment length polymorphism in HLA class II genes of Latin-American Caucasian celiac disease patients

Association of dietary intake and serum concentration of omega-3 fatty acids on celiac disease: evidence from observational study and Mendelian randomization

OBJECTIVE

The association between omega-3 fatty acids (O3FA) and celiac disease lacks sufficient investigation.

METHODS

Utilizing data gleaned from the 2009 to 2014 National Health and Nutrition Examination Survey (NHANES), this research comprises a sample of 13 403 adults, each aged 20 years and above. We conducted a multivariable logistic regression analysis to assess the association between dietary intake of O3FA and celiac disease. Subsequently, a two-sample Mendelian randomization was performed to estimate the unconfounded causal relationship between serum O3FA and celiac disease. The principal analytical strategy utilized the inverse-variance weighted methodology.

RESULTS

In this cross-sectional study, 48 occurrences (0.36%) of celiac disease were encompassed. In the multivariable model, there was no association between dietary intake of O3FA and cases of celiac disease (odds ratio: 1.12, 95% confidence interval: 0.47-2.66, P  = 0.792). However, serum levels of O3FA determined by genetic assay were correlated with celiac disease (inverse-variance weighted, β = 0.2439, P  = 0.0287), with no evidence of horizontal pleiotropy ( P  = 0.3689).

CONCLUSION

The dietary consumption of O3FA did not exhibit an association with the risk of celiac disease in this cross-sectional investigation. However, a correlation between celiac disease and serum levels of O3FA was observed in the Mendelian randomization. Further investigations, including human clinical trials, are warranted.

Human leukocyte antigen class II alleles in white Brazilian patients with celiac disease

BACKGROUND

Celiac disease (CD) is a permanent gluten intolerance disorder characterized by malabsorption, intestinal mucosa villus atrophy, and crypt hyperplasia. Clinical and histologic features improve in persons consuming a gluten free diet. The pathogenesis of CD involves environmental, genetic, and immunologic factors.

METHODS

The frequencies of human leukocyte antigen (HLA) class II alleles were evaluated in white Brazilian patients who had CD and compared with those observed in healthy individuals from the same geographical area (Ribeirão Preto, São Paulo) and of similar ethnic background. Twenty-five patients with CD, 11 females and 14 males, and 91 control individuals were studied. The HLA class II alleles were typed using amplified DNA hybridized with sequence-specific primers. Statistical analysis was performed using the two-tailed Fisher exact test. The relative risk (RR), etiologic fraction (EF), and preventive fraction (PF) were also estimated. The EF represents the attributable risk for the development of CD at the population level, whereas PF represents the protective risk.

RESULTS

The frequency of the HLA-DRB1*03, HLA-DRB1*07, and HLA-DQB1*02 alleles was significantly increased in patients. The RR conferred by these alleles was 5.35, 7.15, and 10.6, respectively, and the EF was 48.7%, 44.7%, and 76%, respectively. The frequency of HLA-DQB1*06 alleles was significantly decreased in CD patients, conferring an RR of 0.08 and a PF of 48%.

CONCLUSIONS

The results show that HLA-DRB1*03, HLA-DRB1*07, and HLA-DQB1*02 alleles conferred susceptibility to CD in Brazilian patients. In contrast, HLADQB1*06 alleles conferred protection against development of the disease.

Synergistic effect of two HLA heterodimers in the susceptibility to celiac disease in Tunisia

The DR and DQ HLA genotypes of 94 Tunisian children affected with celiac disease are analyzed so that we can gain a better understanding of the HLA component of this disease. All of them carry at least one of two specific heterodimers: a DQ heterodimer, encoded by DQA1*0501, DQB1*0201 and/or a DR heterodimer, encoded by the nonpolymorphic gene DRA and the DRB4 gene. Quantifying the relative penetrances of all susceptible genotypes gives evidence for a synergistic effect of these two heterodimers and for a dose effect of the alleles encoding the beta chains of these two heterodimers. The DR3DR7 individuals have the greatest risk. They present the two kinds of heterodimers and carry two DQB1*0201 alleles. Celiac disease is the first HLA-associated disease for which the at-risk genotypes are so well delineated.

Reevaluation of the relative risk for susceptibility to celiac disease of HLA-DRB1, -DQA1, -DQB1, -DPB1, and -TAP2 alleles in a French population

In a population of 46 children with CD recruited in the Paris area of France, an excess of DRB1*03 and DRB1*07 alleles and of DR3/DR7, DR3/DR3 and DR11(or 12)/DR7 phenotypes was found (RRs of 6.3, 9.3, 24.6, 15, and 15.1, respectively), which is reminiscent of the markers of susceptibility observed in southern rather than in northern European celiac patients. More importantly, the highest association with CD was not found in individuals expressing the DQA1*0501-DQB1*0201 heterodimer in single dosage (RR = 24.9) or in homozygous state, but in people co-expressing one copy of DQA1*0501-DQB1*0201 on one haplotype and a second copy of DQB1*0201 on the second haplotype (RR = 35.7). This suggests that in our population either DQB1*0201 or a gene closely linked to DQB1*0201 influences the susceptibility to CD conferred by the DQA1*0501-DQB1*0201 heterodimer. Significant positive or negative RRs conferred by some TAP2 or DPB1 alleles were found. However, they were moderate compared to the RR conferred by the expression of a second copy of DQB1*0201. Moreover, they were no longer significant when patients were compared with HLA-DR matched controls. This suggests that associations of CD with TAP2 and DPB1 alleles are secondary to linkage disequilibria and argues against the contribution of these alleles in resistance and/or susceptibility to CD. Thus the "raison d'être" of a "DQB1*0201 second haplotype effect" in susceptibility to CD remains to be elucidated.

Genetic difference in HLA-DR phenotypes between coeliac disease and transitory gluten intolerance

Genetic differences in HLA phenotypes were studied in coeliac disease to investigate why some patients do not react with mucosal damage after gluten challenge. Forty five children with coeliac disease and 16 with transitory gluten intolerance were typed; 76 subjects served as controls. HLA phenotypes in children with coeliac disease had significantly higher proportions of DR3/X and DR5/7 than controls (48.8% v 11.8% and 26.7% v 5.3%). Children with transitory gluten intolerance had lower DR3/X (43.8%) than children with coeliac disease and there were no DR5/7 phenotypes. Further analysis of similarly well defined cases might show whether genetic differences in the DR3/X and DR5/7 phenotypes can serve as a marker for the permanence of gluten intolerance.

Polymorphism of antigen processing (TAP, LMP) and HLA class II genes in celiac disease

Susceptibility to CD is strongly associated with particular HLA class II molecules. However, additive genetic factors are likely to be required for the development of the disease. The polymorphic TAP and LMP genes, located within the HLA class II region, are involved in the antigen presentation pathway and thus represent candidate susceptibility genes. HLA class II DRB1, DRB3, DQA1, DQB1, and DPB1 as well as TAP1, TAP2, and LMP2 polymorphism was studied in 80 Caucasian CD patients and 213 normal controls by DNA oligotyping. The DQB1*0201 allele was found in 96.3% of CD patients and provided the highest risk (RR = 50), whereas only 89% of CD patients carried the DQ alpha 501/beta 201 heterodimer (RR = 30). The participation of the DRB3 and DPB1 locus was ruled out as it was attributed to a linkage disequilibrium on the DR3 haplotype. TAP1 and LMP2 allelic distribution was not significantly different among CD patients and controls. The TAP2-C allele was completely absent from the CD population, while it was found in 22.5% of controls. Although linkage disequilibrium between TAP2 and class II loci clearly exists in some haplotypes, TAP could act as additional susceptibility genes.

Molecular characterization of HLA class II genes in celiac disease patients of Latin American Caucasian origin

In the present study, the polymorphic domain of HLA class II genes present in a pediatric population of Argentinian celiac disease patients was analyzed by hybridization to sequence-specific oligonucleotides and DNA sequencing. Sixteen out of 16 DR5/7 heterozygous patients bore the DQA1*0501 and DQB1*0201 alleles implicated in the DQ2 risk specificity. The second exon of DQA1, DQB1 and DRB1 genes from 2 DR5/7 patients was characterized by DNA sequencing. The following alleles were found in both patients: DRB1*1101 and DRB1*0701; DQB1*0301 and DQB1*0201; DQA1*0501 and DQA1*0201. Previous serological analysis in this population had shown the presence of DQ2 in 95% of the patients (40% in controls) and a negative association with DQ1 haplotypes, suggesting the presence of other "permissive" or neutral alleles. The following HLA-DQB1 alleles, besides DQB1*0201, were identified in 31 CD patients: DQB1*0301, 0302, 0401 and 0402. All these alleles share a common pattern of residues between positions 84 and 90, and distinct from that present in DQ1-related alleles.

HLA-DQ2 second-domain polymorphisms may explain increased trans-associated risk in celiac disease and dermatitis herpetiformis

Sequence polymorphism in the DQ2 beta chain was investigated in 80 Caucasoid patients with CD, 23 patients with DH, and 64 healthy controls. A set of amplification primers were designed to amplify a 281-bp region between amino acids 95 and 135 encoding the second domain of the DQ beta chain gene. A polymorphism at amino acid 135 was shown to distinguish DR3 and DR7 haplotypes. Two SSO probes were designed to identify amino acid sequences (133-135) RND (DR3-DQ2) and RNG (DR7-DQ2). To establish whether polymorphism existed elsewhere in the second-domain sequence, which could explain the migratory characteristics of the CD-associated DR3-DQ2 beta-chain reported by Roep et al. DQB1 second-domain PCR products were sequenced from the genomic DNA of three CD patients. The results showed that the polymorphism at amino acid 135 distinguishing DR3 and DR7 haplotypes was present in CD, DH patients, or normal controls of the appropriate DR and DQ genotypes by oligonucleotide hybridization. Cloning and sequencing of DQB1 second domains of three CD patients (two DR3,3 and one DR3,7) gave normal sequences expected from their genotypes. No specific polymorphism of DQB1 second domains on CD-associated DR3 haplotypes distinguishes them from normal DR3 haplotypes. We conclude that individuals positive for the DR3,7 genotype have the potential to express a unique trans-encoded heterodimer with enhanced ability to predispose people to CD.

Celiac disease among Ashkenazi Jews from Israel. A study of the HLA class II alleles and their associations with disease susceptibility

The immunogenetics of celiac disease demonstrates a highly significant association with the HLA class II alleles DQA1*0501 DQB1*0201 encoded in either a cis- or trans-configuration. In Northern Europe, these alleles are found in linkage disequilibrium with DRB1*0301 while in Southern Europe an additional secondary association through linkage disequilibrium is seen with the combination DRB1*1101/0701. This study examines 34 Ashkenazi Jews with celiac disease and 36 ethnically matched controls to determine alleles at the DRB, DQA1, DQB1, and DPB1 loci using SSO probes in conjunction with gene amplification by the PCR. The results confirm a highly significant association with the DQA1*0501 DQB1*0201 allelic combination (71% celiac vs 8% control individuals; p = 0.00005; chi 2 = 21.4). Of celiac subjects, 29% were negative for the proposed DQ susceptibility alleles, the majority of whom were DRB1*0402 positive (20% overall celiac group). No additional susceptibility was associated at the DRB3 and DPB loci. This study confirms that the MHC-linked celiac disease susceptibility among Ashkenazi Jews is closely associated with the presence of the combination of alleles DQA1*0501 DQB1*0201. However, within this population of relatively high-prevalence celiac disease, 30% of celiac patients do not carry these alleles and are therefore not covered by a single "unifying" hypothesis.

Polymorphism of the 5' flanking region of the HLA-DQA1 gene in coeliac disease

Coeliac disease (CD) is associated with particular HLA genotypes. The susceptibility gene (or genes) has been mapped to the class II region, most probably to the DQ loci. Polymorphism of the upstream promoter region of the DQA1 gene (QAP) has been recently reported. At least ten variants or QAP alleles have been found, some of which are present in the cis-acting regulatory sequences. Allelic differences in DQ molecule expression may play a role in susceptibility to CD. We investigated the QAP polymorphism in 102 CD patients and 142 unrelated healthy controls of Czech origin using polymerase chain reaction amplification (PCR) of genomic DNA and oligonucleotide probes. We found a significant frequency increase of the alleles QAP 4.1 (RR = 10.3, p.c. = 10(-6) and QAP 2.1 (RR = 2.4, p.c. = 0.017) in patients over controls. An increased susceptibility is provided by the presence of both alleles, as is shown by the higher proportion of QAP 4.1, 2.1 heterozygotes among patients than expected from the Hardy-Weinberg equilibrium and by the comparison of the odds ratios for these alleles. There is a strong linkage disequilibrium between the QAP alleles and the DQA1, DQB1, and DRB1 loci. Two haplotypes carrying the QAP alleles whose frequency is increased are predominant in this group of CD patients: DQB1*0201, DQA1*0501, QAP4.1, DRB1*0301 and DQB1*0201, DQA1*0201, QAP 2.1, DRB1* 0701. Thus, the QAP variants are increased as part of these haplotypes and we cannot discriminate if they are responsible for the primary association.

HLA susceptibility genes in celiac disease: genetic mapping and role in pathogenesis

The overrepresentation of particular HLA alleles in patients with celiac disease was first noted two decades ago. Several lines of evidence obtained during the last years strongly suggest that a particular HLA-DQ heterodimer, encoded by the DQA1*0501 and DQB1*0201 genes in cis or trans configuration, confers the primary disease susceptibility. This paper reviews the evidence behind this concept and discusses how this particular DQ molecule may be involved in the pathogenesis.

On the HLA-DQ(alpha 1*0501, beta 1*0201)-associated susceptibility in celiac disease: a possible gene dosage effect of DQB1*0201

The HLA-associated susceptibility to develop celiac disease (CD) seems mainly to be conferred by a particular HLA-DQ heterodimer encoded by the DQA1*0501 and DQB1*0201 genes either in cis or in trans position. To study the possible influence of DRB1 or other DQA1 and DQB1 alleles on the CD susceptibility conferred by these DQ genes, we performed genomic HLA typing of 94 CD patients, selected those who carried at least one copy of the DRB1*0301-DQA1*0501-DQB1*0201 haplotype (N = 89) and compared them to 47 random, healthy Norwegians matched with the patients to carry at least one copy of the above haplotype. We found an excess of DQB1*0201 homozygosity in the patients. This was due to an increased frequency of the DRB1*0301-DQA1*0501-DQB1*0201 and DRB1*0701-DQA1*0201-DQB1*0201 haplotypes present on the other chromosome. We propose that, in individuals carrying the DQA1*0501 and DQB1*0201 alleles, the presence of a second copy of the DQB1*0201 allele increases susceptibility to CD.

HLA class II alleles associated with celiac disease susceptibility in a southern European population

Susceptibility to celiac disease in Northern Europe is associated with the human leukocyte antigens (HLA) B8, DR3 and DQ2, which exist together on an extended haplotype. The strong predominance of this haplotype within the Northern European celiac populations, together with the linkage disequilibrium which occurs between these loci, does not allow identification of the gene(s) primarily associated with disease susceptibility. Studies from Southern Europe using both serology and examination of restriction fragment length polymorphisms (RFLP) have demonstrated associations with DR3, DR7 and DQ2, suggesting that the DQ locus is primarily involved. We investigated 43 celiac patients and 41 healthy controls from Rome, Italy, using sequence-specific oligonucleotide (SSO) probes, in conjunction with gene amplification by the polymerase chain reaction (PCR), to determine alleles at the DRB, DQA1, DQB1 and DPB1 loci: 19% of celiac patients possessed the alleles DRB1*0301 DRB3*0101, 33% DRB1*0301 DRB3*0201 and 33% of celiac patients were heterozygous for DRB1*1101-1201/DRB1*0701. The strongest association with celiac disease susceptibility was the combination of alleles DQA1*0501 DQB1*0201 (91% celiac patients vs. 12% controls; p = 0.000002). There was no additional susceptibility associated with alleles at the DPB locus. This study confirms the hypothesis that susceptibility is associated with a particular combination of DQ alleles and the ethnic variation in DR frequencies is secondary to linkage disequilibrium with these DQ alleles.

HLA-DP polymorphism in northern Italian celiac patients

The contribution of HLA-DP genes to celiac disease susceptibility has been investigated in 95 Italian patients, 41 with childhood and 54 with adult disease onset. Polymerase chain reaction amplification, sequence-specific oligonucleotide probe hybridization and restriction fragment length polymorphism analyses have been carried out. All celiac patients and 56 out of 128 random healthy controls were DQw2-positive. The frequency of the DPB1*0101 allele was significantly increased (pc = 0.002, relative risk 5.21) in patients with celiac disease (23.2%) compared to the whole panel of controls (5.5%), but not to the 56 controls bearing DQw2 (10.7%). No significant difference in the frequency of DPB1*0101 was found between celiac patients with pediatric (24.4%) or adult (22.2%) onset. The DPB1*0101 allele was associated with both the DR3-DQw2 and DR7-DQw2 haplotypes. Moreover, our study has not confirmed the association with DPB1*0402 and DPB1*0301 previously reported in celiac children from southern Italy. The linkage of the DPB1*0101 allele with the DQ locus and the observation that the DP but not the DQ association appears to be ethnically dependent strongly support a secondary role of DP molecules in celiac disease susceptibility.

A study of Italian pediatric celiac disease patients confirms that the primary HLA association is to the DQ(alpha 1*0501, beta 1*0201) heterodimer

Celiac disease (CD) has been recently reported to be primarily associated with the DQ(alpha 1*0501, beta 1*0201) heterodimer encoded in cis on DR3 haplotype and in trans in DR5,7 heterozygous individuals. The high incidence of DR5,7 heterozygotes, reflecting the high frequency of the DR5 allele in Italy, makes the analysis of the Italian CD patients critical. Polymerase chain reaction-amplified DNA from 50 CD patients and 50 controls, serologically typed for DR and DQw antigens, was hybridized with five DQA1-specific oligonucleotide probes detecting DQA1*0101 + 0102 + 0103, DQA1*0201, DQA1*0301 + 0302, DQA1*0401 + 0501 + 0601, and DQA1*0501 and a DQB1-sequence-specific oligonucleotide probe recognizing DQB1*0201 allele. As expected by the DR-DQ disequilibria, DQA1*0201 [62% in patients versus 26% in controls, relative risk (RR) = 5] and DQA1*0501 (96% versus 56%, RR = 19) show positive association with the disease. Of CD patients, 92% (50% DR3 and 42% DR5,7) compared to 18% of the controls carry both DQA1*0501 and DQB1*0201 alleles, so that the combination confers an RR of 52, higher than both the risks of the single alleles (DQA1*0501 RR = 19, DQB1*0201 RR = 30), confirming the primary role of the dimer in determining genetic predisposition to CD both in DR3 and in DR5,7 subjects.

A high frequency of the A30, B18, DR3, DRw52, DQw2 extended haplotype in Sardinian celiac disease patients: Further evidence that disease susceptibility is conferred by DQ A1*0501, B1*0201

This study characterizes by serological and molecular methods the HLA class I and class II alleles in a group of celiac disease children, their parents and a control group of Sardinian descent. We found the DR3-DQw2 haplotype in all patients which was, in almost all cases (84%), associated with the HLA-A30, B18, DR3, DRw52, DQw2 extended haplotype named "Sardinian haplotype" because of its frequency (12-15%) in this Caucasian population. This is the first time that this DQw2-linked haplotype has been reported with such a high frequency in CD. However, no different distribution of "Sardinian haplotype" was found comparing CD patients with 91 haplotyped DQw2-positive controls. This finding indicates that the DQw2 antigen in Sardinians is almost always associated with the A30, B18, DR3, DRw52, DQw2 extended haplotype. The DQA1 and DQB1 second exon sequence analysis of the B18,DR3 and B8,DR3 haplotypes showed the DQA1*0501 and DQB1*0201 alleles which shared the already published sequences. DPB1 subtyping showed the DPB1*0301 allele more frequently (p less than 0.005) in CD patients but this difference was no longer significant when patients and controls, both heterozygous for the DR3-DQw2 haplotype, were compared. We suggest that the divergent HLA extended haplotypes and DP allele associated with CD, described in different Caucasian populations, can be explained by the particular DQw2 linkage disequilibrium in each population.

Expression of HLA-DQ antigens in the small-intestinal mucosa of patients with coeliac disease

Studies at the DNA and product level of B-cell lines of coeliac patients have shown a strong association between coeliac disease and the HLA-DQ alpha 2.3 and HLA-DQ beta 2.7 alleles. The monoclonal antisera SFR20-DQ alpha 5 and XIII-358.4, which specifically react with HLA-DQ alpha 2.3 and with HLA-DQ beta 2.3 and -DQ beta 2.7, respectively, have been used to detect the expression of these specificities in the small-intestinal mucosa of 7 coeliac patients and 11 non-coeliac persons. An immunoperoxidase technique on frozen tissue sections of jejunal biopsy specimens was used. Positive specimens showed immunoperoxidase staining of lymphocytes and histiocytes in the lamina propria. The epithelial cells showed no immunoperoxidase staining. Positive results at the intestinal level correlated with the HLA typing of the patients and controls. The distribution found for the HLA-DQ alleles in the intestinal mucosa makes the role of a HLA-DQ alpha/beta dimer as gliadin receptor at the epithelial cell less probable, but it is compatible with the hypothesis that these DQ molecules are involved in the regulation of the intestinal immune response to gluten.

Reassessment of HLA association with celiac disease in special reference to the DP association

Patients with the late-onset form of celiac disease have been studied for HLA association by conventional serology (DR and DQ typing) and by oligonucleotide probing with gene amplification (DP typing). Patients and controls were sampled in the Bologna area of northern Italy. Almost all patients were positive for DQw2 (94%), being DR3 positive (72%) and/or DR7 positive (65%). The proportion of DR3/7 heterozygotes in the patients was significantly increased over that expected from the Hardy-Weinberg equilibrium. No positive association with DR5 and no significant increase of DR5/7 heterozygotes were observed. Among the DP alleles reported to exhibit an association with celiac disease in other populations, only DPB3 showed a moderate increase of a borderline significance, not attributable to a linkage disequilibrium with DQw2.

Susceptibility to develop celiac disease is primarily associated with HLA-DQ alleles

We have recently reported that the susceptibility to develop celiac disease (CD) seems to be primarily associated to a particular combination of an HLA-DQA1 (DQA1*0501) and an HLA-DQB1 (DQB1*0201) allele: i.e., a particular DQ alpha/beta heterodimer. To investigate whether certain DP alleles might also contribute to the genetic susceptibility, DPA1 and DPB1 genes of 94 CD patients and 132 healthy controls were examined by probing in vitro amplified DNA with sequence-specific oligonucleotide probes corresponding to all hitherto known DPA1 and DPB1 alleles. The frequencies of the DPA1*0201 and of the DPB1*0101 alleles were increased in CD patients compared to healthy controls (0.31 versus 0.14 and 0.25 versus 0.08, respectively). However, these DP alleles were in linkage disequilibrium with CD-associated DQ alleles in the normal population, and the difference in frequency of these DP alleles was no longer significant when CD patients and healthy controls carrying the CD-associated DQA1*0501 and DQB1*0201 alleles were compared. DQB1*0201 homozygous individuals were overrepresented among DQB1*0201-positive patients compared to controls. When DQB1*0201 heterozygous patients and controls were compared, nearly identical frequencies of the DPA1*0201 and the DPB1*0101 alleles were found. Thus, the observed increase of the DPA1*0201 and DPB1*0101 alleles among CD patients seems mainly to be caused by linkage disequilibrium to the CD-associated DQ alleles.