Dense fine-mapping study identifies new susceptibility loci for primary biliary cirrhosis.

We genotyped 2,861 cases of primary biliary cirrhosis (PBC) from the UK PBC Consortium and 8,514 UK population controls across 196,524 variants within 186 known autoimmune risk loci. We identified 3 loci newly associated with PBC (at P<5×10(-8)), increasing the number of known susceptibility loci to 25. The most associated variant at 19p12 is a low-frequency nonsynonymous SNP in TYK2, further implicating JAK-STAT and cytokine signaling in disease pathogenesis. An additional five loci contained nonsynonymous variants in high linkage disequilibrium (LD; r2>0.8) with the most associated variant at the locus. We found multiple independent common, low-frequency and rare variant association signals at five loci. Of the 26 independent non-human leukocyte antigen (HLA) signals tagged on the Immunochip, 15 have SNPs in B-lymphoblastoid open chromatin regions in high LD (r2>0.8) with the most associated variant. This study shows how data from dense fine-mapping arrays coupled with functional genomic data can be used to identify candidate causal variants for functional follow-up.

Susceptibility to amoxicillin-clavulanate-induced liver injury is influenced by multiple HLA class I and II alleles.

BACKGROUND & AIMS: Drug-induced liver injury (DILI), especially from antimicrobial agents, is an important cause of serious liver disease. Amoxicillin-clavulanate (AC) is a leading cause of idiosyncratic DILI, but little is understood about genetic susceptibility to this adverse reaction. METHODS: We performed a genome-wide association study using 822,927 single nucleotide polymorphism (SNP) markers from 201 White European and US cases of DILI following AC administration (AC-DILI) and 532 population controls, matched for genetic background. RESULTS: AC-DILI was associated with many loci in the major histocompatibility complex. The strongest effect was with an HLA class II SNP (rs9274407, P=4.8×10(-14)), which correlated with rs3135388, a tag SNP of HLA-DRB1*1501-DQB1*0602 that was previously associated with AC-DILI. Conditioned on rs3135388, rs9274407 is still significant (P=1.1×10(-4)). An independent association was observed in the class I region (rs2523822, P=1.8×10(-10)), related to HLA-A*0201. The most significant class I and II SNPs showed statistical interaction (P=.0015). High-resolution HLA genotyping (177 cases and 219 controls) confirmed associations of HLA-A*0201 (P=2×10(-6)) and HLA-DQB1*0602 (P=5×10(-10)) and their interaction (P=.005). Additional, population-dependent effects were observed in HLA alleles with nominal significance. In an analysis of autoimmune-related genes, rs2476601 in the gene PTPN22 was associated (P=1.3×10(-4)). CONCLUSIONS: Class I and II HLA genotypes affect susceptibility to AC-DILI, indicating the importance of the adaptive immune response in pathogenesis. The HLA genotypes identified will be useful in studies of the pathogenesis of AC-DILI but have limited utility as predictive or diagnostic biomarkers because of the low positive predictive values.

Genome-wide association study identifies 12 new susceptibility loci for primary biliary cirrhosis.

In addition to the HLA locus, six genetic risk factors for primary biliary cirrhosis (PBC) have been identified in recent genome-wide association studies (GWAS). To identify additional loci, we carried out a GWAS using 1,840 cases from the UK PBC Consortium and 5,163 UK population controls as part of the Wellcome Trust Case Control Consortium 3 (WTCCC3). We followed up 28 loci in an additional UK cohort of 620 PBC cases and 2,514 population controls. We identified 12 new susceptibility loci (at a genome-wide significance level of P < 5 × 10⁻8) and replicated all previously associated loci. We identified three further new loci in a meta-analysis of data from our study and previously published GWAS results. New candidate genes include STAT4, DENND1B, CD80, IL7R, CXCR5, TNFRSF1A, CLEC16A and NFKB1. This study has considerably expanded our knowledge of the genetic architecture of PBC.

Human leucocyte antigen class II genotype in susceptibility and resistance to co-amoxiclav-induced liver injury.

BACKGROUND & AIMS: Co-amoxiclav is one of the most common causes of drug-induced liver injury (DILI). Although there are previous reports of genetic associations between HLA class II and co-amoxiclav-related DILI, studies to date have been based on very small numbers from single centres only. In order to address this problem we have investigated the role of HLA class II DRB1 and DQB1 in 61 cases of co-amoxiclav DILI as part of a UK-wide multicentre study. METHODS: HLA alleles and genotypes were compared with those of 40 individuals exposed to co-amoxiclav without toxicity (treated controls) and 191 population controls. RESULTS: There were two significant findings from the study. First, HLA-DRB1*15 was increased in patients (53%) versus both treated (33%: OR=2.29: 95% CI: 1.00-5.26) and population controls (30%: OR=2.59:95% CI: 1.44-4.68: p=0.002). Second, DRB1*07 was found to be reduced in patients (9.8%) compared to both treated (35%: OR=0.18: 95% CI: 0.06-0.52: p=0.0011, pc=0.0154) and population controls (29%: OR=0.266: 95% CI: 0.11-0.65: p=0.0019, pc=0.0266). CONCLUSIONS: These results confirm the previously reported significant genetic risk for HLA-DRB1*15 and also provide evidence of a protective effect of the HLA-DRB1*07 family of alleles. HLA alleles and haplotypes may be particularly important in susceptibility and resistance to co-amoxiclav-DILI, but it remains to be seen whether this effect is due to the identified alleles or others in close linkage disequilibrium elsewhere on the MHC.

HLA-B*5701 genotype is a major determinant of drug-induced liver injury due to flucloxacillin.

Drug-induced liver injury (DILI) is an important cause of serious liver disease. The antimicrobial agent flucloxacillin is a common cause of DILI, but the genetic basis for susceptibility remains unclear. We conducted a genome-wide association (GWA) study using 866,399 markers in 51 cases of flucloxacillin DILI and 282 controls matched for sex and ancestry. The GWA showed an association peak in the major histocompatibility complex (MHC) region with the strongest association (P = 8.7 x 10(-33)) seen for rs2395029[G], a marker in complete linkage disequilibrium (LD) with HLA-B*5701. Further MHC genotyping, which included 64 flucloxacillin-tolerant controls, confirmed the association with HLA-B*5701 (OR = 80.6, P = 9.0 x 10(-19)). The association was replicated in a second cohort of 23 cases. In HLA-B*5701 carrier cases, rs10937275 in ST6GAL1 on chromosome 3 also showed genome-wide significance (OR = 4.1, P = 1.4 x 10(-8)). These findings provide new insights into the mechanism of flucloxacillin DILI and have the potential to substantially improve diagnosis of this serious disease.

Genomic polymorphism at the interferon-induced helicase (IFIH1) locus contributes to Graves' disease susceptibility.

CONTEXT: A recent large-scale analysis of nonsynonymous coding polymorphisms showed strong evidence that an alanine to threonine amino acid change at codon 946 of the interferon-induced helicase (IFIH1) gene (SNP ID rs1990760) was associated with type 1 diabetes. Previous investigations have also demonstrated that an intronic polymorphism (termed PD1.3; SNP ID rs11568821) in the programmed cell death (PDCD1) gene was associated with systemic lupus erythematosus and rheumatoid arthritis. OBJECTIVE: We sought to replicate these genetic associations in Graves' disease and autoimmune Addison's disease patient cohorts. PATIENTS AND METHODS: A total of 602 Graves' disease subjects, 214 Addison's disease subjects, and 446 healthy controls were genotyped for the IFIH1 and PDCD1 single-nucleotide polymorphisms using mass spectrometer analysis of primer extension products (Sequenom). RESULTS: The alanine-carrying allele at the IFIH1 codon 946 polymorphism was present in 796 of 1204 (66%) Graves' disease patient alleles compared with 508 of 892 (57%) control subject alleles [odds ratio 1.47 (5-95% confidence interval, 1.23-1.76); P = 1.9 x 10(-5)]. In contrast, there was no association of alleles at this marker in autoimmune Addison's disease. Neither was there evidence for association in either patient cohort at the PD1.3 polymorphism. CONCLUSIONS: We confirm a significant contribution of the Ala946Thr IFIH1 polymorphism to organ-specific autoimmune diseases, extending the range of conditions associated with this variant to include Graves' disease. This polymorphism may also contribute to several other autoimmune disorders.

HLA class II alleles, genotypes, haplotypes, and amino acids in primary biliary cirrhosis: a large-scale study.

Twin and family studies suggest there is a significant genetic component to primary biliary cirrhosis (PBC). However, the inability to replicate reported associations has been a recurring problem, with the only consistently reported genetic association that between PBC and HLA-DRB1*0801. However, recently even this has been questioned, and a number of novel associations have also been reported. We reinvestigated HLA class II DRB1, DQA1, and DQB1 alleles and haplotypes in a total of 492 well-characterized PBC patients, 412 from the United Kingdom and an additional 80 patients from northern Italy. There was a clear and significant association with HLA-DRB1*0801 in both groups of patients compared to population-specific healthy controls (12% versus 4% in the UK patients, P=.00087, OR=3.05; and 18% versus 6% in the Italian patients, P=.021, OR=3.15). There were also significant protective associations with DRB1*11 in the Italian patients (28% versus 47%, P=.0071, OR=0.42), but not in the UK patients (8% versus 8%) and a protective association with DRB1*13 in both series (14% versus 20%, P=.042, OR=0.65 in the UK patients; and 10% versus 31%, P=.00092, OR=0.25 in the Italian patients). In conclusion, a complex relationship exists between HLA and PBC, and some genetic associations may be population specific.

Frequency and significance of antibodies to Saccharomyces cerevisiae in autoimmune hepatitis.

Our aims were to determine the frequency of antibodies to Saccharomyces cerevisiae in autoimmune hepatitis and assess associations with concurrent mucosal diseases, genetic factors, and corticosteroid response. Seropositivity was determined by enzyme immunoassay in 385 samples obtained from 178 patients. Antibodies to Saccharomyces cerevisiae were detected in 49 patients (28%), and serum levels of immunoglobulin A were higher in seropositive patients (410 +/- 35 versus 321 +/- 20 mg/dL; P = 0.02). Individuals with and without antibodies were not otherwise distinguished by concurrent mucosal diseases, laboratory findings, or outcomes. Antibodies to tissue transglutaminase occurred more commonly in seropositive patients (16 versus 4%; P = 0.008), but this association was lost when corroborating serological criteria for celiac disease were sought. We conclude that antibodies to Saccharomyces cerevisiae are common in autoimmune hepatitis. They may be associated with non-disease-specific immune responses, but they do not define individuals with a distinctive clinical phenotype, associated mucosal diseases, or treatment outcome.

Genetic factors in the pathogenesis of primary biliary cirrhosis.

Current knowledge of the genetic basis of PBC is at best incomplete and at worst poor. Studies so far may be used as a guide to the pitfalls that await unwary investigators and also in deciding where to look and which genes or systems are most likely to yield informative results. The Human Genome Project has revealed a vast array of polymorphism that is too much to contemplate even with the best of current techniques. The crucial processes are the selection of candidates and study design. The strong genetic associations so far in PBC are with chromosomes 6p21.3 and 2q and include; HLA DRBI*08 haplotypes, CTLA4* G and IL1RN-IL1B haplotypes, CASP8, and nramp1. Many of the latter should be considered with caution until confirmed in independent series. Other associations with MBL, APOE and VDR remain to be confirmed. There are also several informative negatives, MMP3 and IL10 for example. It is unlikely that the only genes that influence disease susceptibility and progression in PBC are immunoregulatory genes concerned with T cell immunity. Recent studies indicate a new era for immunogenetics, when genes encoding all immune active proteins may be considered as candidates. One should not concentrate solely on the immune response as recent investigations of mannose binding lectin and apolipoprotein-E testify. One is only just beginning to understand the genetic basis of complex diseases like PBC. The key issues for future investigators are: defining the mechanisms where by self tolerance is broken, defining the mechanisms that determine the rate of disease progression, and identifying genetic markers to predict progression and malignancy. Assessing the genetic basis of variability in disease progression. The significant variation in rate of progression of PBC has led to the hypothesis that genes, in addition to contributing to disease susceptibility, may also determine the rate of disease progression. Several of the studies mentioned earlier have suggested associations between alleles at polymorphic loci and rate of progression . All studies performed to date, however, have been retrospective in nature. One problem inherent in such studies is that of definition of disease progression. One simple definition, that of histological progression to Scheuer stage IV disease , requires liver biopsy. The need to perform repeat biopsies raises ethical problems in cases where there is no other clinical indication. Studies of histologic progression in patients in the control arm of therapeutic trials represent one scenario where repeat biopsy would be indicated. However, the typical time course of such trials is 2 years, insufficient for meaningful assessment of disease progression and natural history, particularly in PBC where there is marked heterogeneity and, as a result, tissue sampling error. Yet, alternative systems for assessing disease progression, such as the Mayo prognostic score, lack sensitivity in any scenario other than existing advanced disease. Outlook for the future. Clinical observations support a significant genetic component to disease susceptibility. Elucidating predisposing genetic associations will markedly assist in understanding the pathophysiology of disease. Investigations to date have been restricted to various community-based case-control association studies, with well-recognized limitations. In future SNP maps and haplotype maps from the Human Genome Project will be available. Studies will require the collection of several well-characterized patients. To meet the required statistical power this will necessitate collaboration on a national and international scale. It is essential that these studies address the relationship between genes and disease progression. The possibility of identifying, in the early stages of disease, patients who are at elevated risk for more rapid progression, would have obvious clinical benefit in terms of patient management and therapy.

Frequency and nature of cytokine gene polymorphisms in hepatocellular carcinoma in Hong Kong Chinese.

BACKGROUND: The genetic basis of susceptibility to hepatocellular carcinoma (HCC) is poorly understood. Genomic DNA was available from 98 patients with HCC, 77 familial controls, 97 controls from Hong Kong and 96 Northern European controls (NECs). METHODS: Polymorphisms of interleukin (IL)-1beta; IL-1 receptor antagonist (IL-1RN); IL-10 promoter (positions -1082, -819, and -592); and tumor necrosis factor (TNF)-alpha promoter (TNF-a -238 and -308) were investigated. RESULTS: There was marked restriction in the distribution of the IL-1beta and IL-1RN genotypes among Chinese subjects with a predominance of the IL-1beta*1,1 and IL-1RN*1,1 (for unrelated controls compared with NECs only for IL-1beta: chi2 = 15.32, Pc = 0.000091 and for IL-1RN: chi2 = 16.08, Pc = 0.000061). For IL-10, the distribution of alleles was reversed in Chinese vs NECs. The TNFA*2 allele (TNFA -308 A), which is associated with high TNF-alpha production both in vivo and in vitro, was found in <10% of Chinese but was present in 33% of NECs (chi2 = 21.52, Pc <0.0000035). CONCLUSION: Though this study failed to highlight specific associations between any of the polymorphisms tested and the HCC in Hong Kong Chinese, the differences in the distribution of tested alleles may, in part, account for the increased susceptibility of the Chinese population to develop HCC.

Genetics in autoimmune hepatitis.

Current hypotheses suggest that autoimmune hepatitis (AIH) is triggered by an environmental factor in a genetically susceptible host. Multiple genes may interact to produce a "permissive gene pool" that determines both disease risk and phenotype. Studies of type 1 AIH have focused on the major histocompatibility complex (MHC), mapping susceptibility to the DRB1 region. Three different molecular models have been proposed based on histidine at DRbeta13, lysine at DRbeta71, and valine at DRbeta86. Although the lysine-71 model has been adapted to explain data from several other studies, the DRbeta13 and DRbeta86 models are exclusive to their founder populations. It is possible that all three models apply and that the different associations reflect the "molecular footprint" of the common environmental triggers in the different study populations. Studies outside the MHC have identified the CTLA4 A+49G, G allele as a possible second risk allele. There are many neutral polymorphisms in the genome, and further studies are currently needed to identify other disease alleles in type 1 AIH.

Genetic effects on susceptibility, clinical expression, and treatment outcome of type 1 autoimmune hepatitis.

Currently, three genetic factors have been short-listed as possible modulators of susceptibility and severity in type 1 AIH. They are female sex, HLA DRB alleles encoding lysine at position DR beta 71, and the CTLA4*G allele. The fourth association (i.e., TNFRSF6) remains to be confirmed. There are many other candidates to investigate. Current hypotheses suggest that the autoimmune genotype will include multiple (some linked, others discrete) loci which make a permissive background. Not all "at risk" individuals will develop clinical disease, and selection will depend on the interaction of this "permissive gene pool" (i.e., the host) with the environment. The resulting autoimmune phenotype will depend on gene dose and gene interaction. The human genome project has presented medical science with the challenge to identify the genes that determine common human diseases, including autoimmunity [1]. Although type 1 AIH is considerably less common than diabetes or RA, it may serve as a useful model for other autoimmune diseases. Diagnosis depends on histologic findings, and liver biopsy examinations are part of the usual assessment strategy in type 1 AIH. The availability of these tissue specimens provides a clear basis for monitoring disease progression and may permit investigators to study the impact of genetic polymorphism on disease activity. The emergence of high throughput technologies will significantly enhance our ability to study the interactions between constellations of polymorphic genes and both disease expression and behavior. An abundance of polymorphism is found in the genome. In many diseases, functional studies and genome scanning have helped revise and reduce the list of candidates. Affected families are rare in type 1 AIH, and patients are at risk if corticosteroid treatment is withheld. Under these circumstances, genetic studies may be the most practical, low risk means to investigate the pathogenesis of type 1 AIH and many other autoimmune diseases.

Genetic bases of autoimmune hepatitis.

Our goal was to review the hypotheses in evolution that promise to elucidate the genetic bases of autoimmune hepatitis. DRB1*0301 and DRB1*0401 are the principal risk factors in Britain and the United States. Other susceptibility alleles in different ethnic groups commonly share the same or a similar motif at the critical DRbeta71 position of the HLA class II molecule. Disease severity may be determined by the number of alleles encoding lysine at the DRbeta1 position, the density of dimers presenting antigen, and the avidity of T-cell receptors for the displayed antigen. Concurrence on the same or different chromosomes of other nonspecific autoimmune promoters may also contribute. A negatively charged residue at the P4 position of antigenic peptides is preferred for binding to the disease-susceptibility alleles, and this complex may be recognized by promiscuous T cells. We conclude that autoimmune hepatitis is a model by which to study the genetic bases of autoimmunity.

Interleukin-1, interleukin-10 and tumour necrosis factor-alpha gene polymorphisms in hepatitis C virus infection: an investigation of the relationships with spontaneous viral clearance and response to alpha-interferon therapy.

BACKGROUND/AIMS: Though there is a consensus that the HLA DQB1*0301 allele is important in untreated HCV clearance, this association is not universal and a number of genes outside the major histocompatibility complex may also play a role in host responses to HCV infection. Prime candidates, at present, are the genes encoding pro-inflammatory and immuno-regulatory cytokines. The aim of this study was to investigate the relationship between a number of these candidate genes and both spontaneous and treatment related clearance of hepatitis C virus infection. METHODS: Three members of the interleukin-1 gene family: IL-1A, IL-1B and IL-1RN, three polymorphic sites in the interleukin-10 gene promoter (- 1082, - 819, - 592) and two in the tumour necrosis factor-alpha promoter (- 308, - 238) were studied in two independent DNA banks, each with appropriate controls. Standard PCR-based genotyping techniques were used. RESULTS: No significant difference in the distribution of any of the polymorphisms was found in either study set. CONCLUSIONS: These findings in two large groups suggest that future investigations should focus on other candidate genes and may support the view that MHC-encoded susceptibility to chronic HCV infection may be determined by MHC class II rather than MHC class III genes.

Gender effects and synergisms with histocompatibility leukocyte antigens in type 1 autoimmune hepatitis.

OBJECTIVES: Our goals were to determine the effect of gender on the clinical features and treatment outcome of type 1 autoimmune hepatitis, and to assess synergisms with the known genetic risk factors. METHODS: Clinical findings and treatment outcomes were compared in 144 women and 41 men who were also assessed for HLA DR3, HLA DR4, HLA DR3 and DR4 alleles, and the DRB1*1501-DQA1*102 haplotype by polymerase chain reaction. A total of 102 healthy men and women were similarly typed. RESULTS: Women were distinguished from men by higher frequencies of concurrent immune diseases (34% vs 17%, p = 0.05) and HLA DR4 (49% vs 24%, p = 0.007), as had been previously reported. Women, however, had a higher occurrence of non-DRB1*0401 DR4 alleles than men (15% vs 0%, p = 0.02), and men had a lower frequency of these alleles than did normal male subjects (0% vs 16%, p = 0.04). Men and women responded similarly to therapy. Treatment failure occurred more frequently in men only if they had HLA DR3 and women had HLA DR4 (25% vs 4%, p = 0.01). The DRB1*1501-DQA1*102 haplotype did not affect outcome. CONCLUSIONS: Gender influences susceptibility and clinical manifestations, but not outcome. Women have HLA DR4 more commonly than men, but this difference relates to their higher frequency of non-DRB1*0401 DR4 alleles. Female gender may promote risk associated with different HLA DR4 alleles.

Clinical distinctions and pathogenic implications of type 1 autoimmune hepatitis in Brazil and the United States.

BACKGROUND/AIMS: Type 1 autoimmune hepatitis has a strong genetic predisposition that varies among different ethnic groups. Our aims were to determine if the clinical manifestations differed between patients with type 1 autoimmune hepatitis from Brazil and the United States and if classical disease could be associated with region-specific susceptibility markers. METHODS: The clinical manifestations and genetic risk factors of 161 patients from the United States were compared to those of 115 patients from Brazil. RESULTS: The patients from Brazil had earlier disease onset, lower frequency of concurrent immune diseases, higher serum levels of aspartate aminotransferase and gamma-globulin, greater occurrence of smooth muscle antibodies, and lower frequency of antinuclear antibodies than the patients from the United States. Human leukocyte antigen (HLA) DR13 and DRB1*1301 occurred more commonly in the Brazilian patients and HLA DR4 less often. Normal subjects from each country had similar frequencies of HLA DR13 and DR3. CONCLUSIONS: Type 1 autoimmune hepatitis in Brazil has different features at presentation than the disease in Caucasoid patients from the United States, and it is associated with HLA DR13. Background populations in each country have similar frequencies of HLA DR13 and DR3, and region-specific etiologic factors may determine the HLA association.

HLA and cytokine gene polymorphisms in biliary atresia.

BACKGROUND/AIMS: Extrahepatic biliary atresia remains one of the major hepatic causes of death in early childhood. Though a number of hypotheses have been developed to account for this disease, its aetiopathogenesis is poorly understood. One possibility is that this is an immune mediated disease which occurs following either toxic or infectious insult in a genetically susceptible host. Earlier studies suggested weak HLA associations but these remain unconfirmed. More recently studies of viral and autoimmune liver disease have begun to investigate non-MHC immunoregulatory gene polymorphisms. METHODS: In the present study we used molecular genotyping to investigate selected HLA A, B, DRB1, DQA1, DQB1 and DPB1 alleles as well as polymorphisms in the interleukin-1 gene family, interleukin-10 promoter sequence and tumour necrosis factor alpha promoter genes in 101 children referred for surgical assessment with extra hepatic biliary atresia. Genotyping data were compared with those of 134 racially and geographically matched healthy adult health care workers. RESULTS AND CONCLUSIONS: Overall there were no statistically significant differences in the distribution of any of the genes tested comparing patients and controls. These data suggest that biliary atresia is not an HLA-associated disease and that polymorphisms in both the interleukin-1 and interleukin-10 genes are not risk factors for this disease.