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Supported by National Institutes of Health grant DK056839.
Primary biliary cirrhosis (PBC) is an autoimmune biliary disease characterized by injury of small and medium size bile ducts, eventually leading to liver cirrhosis and death. Although the causes remain enigmatic, recent evidence has strengthened the importance of genetic factors in determining the susceptibility to the disease. Besides the strong heritability suggested by familial occurrence and monozygotic twins concordance, for decades there has not been a clear association with specific genes, with the only exception of a low risk conferred by a class II human leukocyte antigen (HLA) variant, the DRB1*08 allele, at least in some populations. The picture has become more complete when strong protective associations between PBC and the HLA DRB1*11 and DRB1*13 alleles were found in Italian and UK series. However, HLA genes have begun again to attract interest thanks to recent genome-wide association studies (GWAS), which clearly demonstrated that the major components of the genetic architecture of PBC are within the HLA region. As expected in a genetically complex disease, GWAS also identified several novel non-HLA variants, but it is worth noting that all of them are in immuno-related genes. In this review, the paradigmatic tale of what, and how, we learned about HLA genes in PBC will be retraced with particular focus on how GWAS are enabling a rewriting the story of PBC pathogenesis. These recent discoveries will not only drive functional studies but will also hold the promise of developing novel disease-specific treatments. (HEPATOLOGY 2011;)
Primary biliary cirrhosis (PBC) is a chronic cholestatic liver disease characterized by progressive destruction of small and medium size intrahepatic bile ducts, leading to cirrhosis and ultimately liver transplantation or death.1 PBC has an estimated prevalence of 1 in 1000 in women over the age of 40, and ursodeoxycholic acid is the only approved therapy.2 The pathogenesis of PBC is clearly autoimmune,3 as indicated by specific serum- and cell-mediated responses against defined epitopes of self antigens, and by a striking female predominance (female-to-male ratio of approximately 10 to 1). In addition, epidemiological data indicate that family members of patients have an increased risk of developing PBC or another autoimmune disorder. On the basis of these considerations, the current hypothesis on the etiopathogenesis of PBC implies that this disease is the result of a genetic predisposition that is permissive for a still unknown environmental agent, possibly xenobiotic or infection.1
For decades, PBC has been considered to have a unique genetic background when compared to other autoimmune diseases because of the strong familial clustering but weak associations with genetic polymorphisms.4 Indeed, despite numerous candidate-gene association studies that were performed, no conclusive data on specific genes have been obtained. In addition, it is worth noting that linkage analysis was poorly feasible in PBC based on the advanced age at diagnosis and the rarity of the disease. In contrast, recent evidences have strengthened the importance of genetic susceptibility in determining disease onset and severity, including a role for sex chromosome abnormalities in affected women5, 6 and high concordance for disease in monozygotic twins.7
The human leukocyte antigen (HLA) loci, located in the major histocompatibility complex (MHC), are the most genetically diverse loci in the human genome8 (Fig. 1). HLA genes encode cell-surface molecules that by means of peptide presentation mediate key immunological events, such as definition of self-tolerance or cellular immune responses to tumors and pathogens.9, 10 Similar to other genetically complex diseases,11 HLA has been extensively studied in PBC, but for decades data have cumulatively suggested only a weak association with the class II HLA DRB1*08 allele.4 This was likely because early studies had several potential limitations: (1) insufficient statistical power due to inadequate sample sizes, (2) lack of careful matching between cases and controls, (3) earlier studies did not rely on molecular analysis, and (4) multiple replications have rarely been carried out.
To overcome all these flaws, our group evaluated the HLA polymorphisms in the largest PBC series ever reported12, 13 and provided evidence not only that PBC susceptibility is associated with the HLA DRB1*08 allele but also that DRB1*11 and DRB1*13 confer strong protection from the disease. Importantly, a few months later, the same protective HLA alleles were confirmed to be associated with PBC in a large-scale case–control study from the UK.14 Because both these protective alleles are known to influence the penetrance of infectious agents, they have implications in light of the proposed infectious theory of PBC origin. However, the revived interest for HLA genes in PBC arising from these studies was soon overcome by three recent genome-wide association studies (GWAS) in PBC, which showed that the strongest associations are located in the HLA region.15-17
This review does not attempt to summarize the knowledge of the genetics of PBC, but will mainly focus on older and more recent associations with HLA variants obtained with candidate-gene large-scale studies and GWAS, and on how these data may change the genetic landscape of PBC.
CTLA-4, cytotoxic T-lymphocyte antigen-4; GWAS, genome-wide association studies; HLA, human leukocyte antigen; IL, interleukin; IKZF3, IKAROS family zinc finger 3; IRF5, interferon regulatory factor 5; ORMDL3, ORM1 like 2; PBC, primary biliary cirrhosis; SNP, single-nucleotide polymorphism; SPIB, SPi-B transcription factor; STAT4, signal transducer and activator of transcription 4; TNF, tumor necrosis factor.
Highlights of Genetic Predisposition in PBC
In the past, a number of reports have reported an increased risk of developing PBC within family members of affected individuals, a scenario called “familial PBC”.18 The majority of these studies as well as population-based epidemiological reports were performed in the UK.19-22 In this geographical area, the former reported rates of PBC prevalence within family members were approximately 1%-2.4%.19, 20 Prevalence rates of familial PBC were later reported to be 6.4% in the UK22 and between 3.8% and 9.0% in a number of studies from North America, Europe, and Japan. A further estimate of the familial prevalence of PBC, the sibling relative risk, was found to be 10.5% in a UK study.22 In addition, a recent large US study indicated that having a first-degree relative with PBC was significantly associated with increased risk of disease, with an odds ratio of 10.7.23 Of course, shared environmental factors by family members may well explain these findings, as suggested by data on prevalence and incidence of PBC.
A role for genetics is also suggested by the frequent coexistence with other autoimmune diseases in more than one-third of patients who have PBC.23 Diseases that may coexist in patients with PBC or family members include rheumatoid arthritis, Sjögren syndrome, and autoimmune thyroid disease.23 The current explosion of new information about these autoimmune diseases allows the identification of a number of common genes underlying multiple diseases.11
Disease concordance rate in monozygotic twin pairs (the proportion of affected pairs concordant for the disease) is another powerful tool to estimate the impact of genetic factors in susceptibility to complex disorders, including autoimmune disorders.11 In the past, PBC concordance rate has been limited to two reports,24, 25 one in a concordant and one in a discordant pair of twins, but monozygosity was not genetically proven. Thanks to a worldwide effort, we were able to identify eight monozygotic and eight dizygotic twin pairs in which at least one subject was affected by PBC and to find a concordance rate of 63%, the highest among autoimmune diseases.7 In the general attempt to dissect the effects of different exposure to environmental factors, we also explored classical epigenetic factors in sets of PBC-affected twins, but excluded their major role in PBC development.26
A role for genetics in PBC is also suggested by animal models of human PBC.27 Most of them are indeed spontaneous murine models due to a number of different genetic changes. The genetically determined models of PBC include the interleukin-2 (IL-2) receptor alpha deleted (IL-2Rα−/−), transforming growth factor beta (TGF-β) receptor II dominant-negative (dnTGF-betaRII), scurfy, nonobese diabetic (NOD) c3c4, and AE2 gene-disrupted (AE2a,b−/−) mice. For one of these models (the IL-2 receptor alpha deleted), there has been a corresponding PBC-like disease reported in a child with IL-2 receptor alpha (CD25) deficiency.28
The literature on PBC contains many publications that have attempted to identify genes with a role in disease susceptibility and progression by evaluating small numbers of variants in one or a few specific candidate genes by means of case–control study designs. Of course, most of these genes code for immune-related molecules and were already implicated in other autoimmune disorders, including tumor necrosis factor (TNF), cytotoxic T lymphocyte antigen-4 (CTLA-4), Toll-like receptors, caspase-8, vitamin D receptor, interleukins IL-1, IL-2, and IL-10, and numerous cytokine and chemokine receptors. However, such approaches have led to very few insights into the genetic basis of PBC, mainly for lack of robust replication. A paradigmatic example is that related to CTLA-4 gene association studies. Although two earlier studies from the UK29 and China30 found a single-nucleotide polymorphism (SNP) associated with PBC, more recent data from Brazil,31 Italy,32 Germany,33 the UK,34 and the US35 failed to confirm it. In addition, the follow-up study by the UK group34 failed to replicate their original positive finding,29 whereas the follow-up study by the US group36 found a novel SNP association in contrast with their original negative finding.35 Accordingly, caution is suggested when interpreting these findings. In the future, candidate gene studies, of course with appropriate size and replication, should focus on dissecting interaction between risk loci, on investigating variants frequencies in different geographical areas, and on risk loci influencing outcomes, treatment response, and symptoms. In this regard, laudable examples are the recent study by Lazaridis and coworkers which showed that a TNF gene variant amplifies a CTLA-4 genotype risk for PBC by examining the possible interaction between these two risk variants.37 The same authors also suggested an interaction between CTLA-4 and programmed cell-death 1 gene variants.35 In addition, because the genetic background may greatly vary among different ethnic groups, our group evaluated the association of other candidate genes in PBC by comparing multiple cohorts from different ethnic populations.38, 39 Finally, a recent French study reported that the progression rate of liver disease under ursodeoxycholic acid therapy was significantly linked to variants of TNF and AE2 genes.40
Clinical awareness of PBC has greatly increased over the past 50 years, laboratory diagnosis is far more precise, and therapy is more effective, yet the main reasons for the female preponderance of PBC have remained unclear.41 We recently proposed that the presence of defects in sex chromosomes might explain both the disproportionate female affliction with PBC and the genetic predisposition to the disease. Indeed, we first reported an age-dependent enhanced monosomy X in the peripheral blood cells of women with PBC,5 later reported that one X chromosome is preferentially lost,6 and finally reported that epigenetic factors influencing PBC onset are more complex than methylation differences at X-linked promoters.26
HLA Associations and PBC
The HLA is one of the most widely studied regions in the human genome and certainly contains valuable genetic information of many complex genetic diseases that have yet to be fully dissected.42-47 HLA genes are located on the short arm of chromosome 6 (6p21.31), with an extension of approximately 3.6 mega–base pairs, and consists of three subregions: the two telomeric class I, class III, and the centromeric class II regions (Fig. 1). The true role of the various HLA alleles in inducing autoimmune reactions remains largely unclear, and the underlying mechanisms might be numerous.48 Among them, it has been suggested that certain HLA alleles are less efficient at presenting self peptides to developing T cells in the thymus, with failure of negative selection. In particular, it is possible that certain HLA molecules present peptide at an “intermediate level”, thus being recognized by T cells without inducing tolerance. Indeed, most self peptides are presented at levels below that which is needed to engage effector T cells, whereas others induce clonal deletion and anergy as presented at high levels. Alternatively, it is possible that specific HLA alleles enhance autoimmune activation by enhancing immunogenicity and influencing the expressed repertoire of T cells.
In fact, the HLA region contains many loci that are largely involved in inflammatory responses, such as MHC class I chain genes A and B, TNF-α, heat-shock proteins, complement component 2, and transporter associated with antigen processing (Fig. 1). Variants of HLA genes have been found to be associated with almost every known complex genetic disease. However, it has been difficult to identify genetic variants within HLA that are directly linked to the cause of diseases; the main reasons for these difficulties are listed and discussed below.
The Old Evidences: Little Interest for HLA.
In the past, a number of studies have evaluated the association of HLA class I variants with PBC susceptibility,49-55 but no significant results were found (Table 1). Several reasons could explain this lack of association. First, the small number of patients evaluated in each study (ranging between n = 21 and n = 75) may account for an inadequate statistical power for comparisons. Second, it must be remembered that in the past only limited members of HLA class I alleles could have been assessed because of the technical methods available at that time, resulting in a risk of underestimating the existing associations. Finally, linkage disequilibrium may well explain why HLA class I gene associations with PBC, as well as with many other autoimmune diseases, are in general not striking.4, 71 Because of these major flaws, a few years ago our group examined the association with HLA class I variants in a large Italian cohort of patients with PBC and controls and reported that PBC is associated with various HLA-B alleles68 (Table 1). However, these associations should be regarded as weak, being present only in a small proportion of our. In the future, HLA class I variants still need to be replicated in different ethnic groups, of course with adequate sample size and study design. Indeed, it could be assumed that similar to the epidemiological data, the genetic background in PBC could be associated with a geographical pattern. It is interesting to note that we are witnessing a resurgence of interest in these gene variants because of their critical function as ligands for killer immunoglobulin-like receptors on natural killer cells and various T lymphocytes.72
Table 1. Synopsis of HLA Association Studies in PBC
Many studies have reported associations of HLA class II alleles and PBC in populations of Caucasian and Asian ethnicity (Table 1). The association with HLA DRB1*08 allele has been found most frequently among reported studies from Germany, the US, Spain, and Sweden, thus indicating that this allele might constitute a risk factor for PBC among Caucasians.54, 56, 63, 67, 69 However, it notable that several European studies have failed to confirm an association with DRB1*08.31, 52, 55, 62, 68 Other than the DRB1*08 variant, associations have been reported with DR349, 55 or DPB1*0301.64 In 2003, we suggested that the DRB1*11 allele has a protective effect against PBC in the Italian population.68 A UK study reported that the linkage of the DQA1*0401 allele and the DR8-DQB1*0402 haplotype is associated with disease progression but not initial susceptibility,66 whereas a more recent US study demonstrated an association between DRB1*08-DQA1*0401-DQB1*04 haplotype and PBC, albeit in a minority of patients.69 Among populations of Asian ethnicity, studies from Japan failed to find a consistent picture of HLA class II associations with PBC,50, 51, 60 with an association between PBC and DR2 in one,50 DPB1*0501 in another,60 and DRB1*0803 in a third.51 However, although there was a lack of consistent associations between specific DRB1 alleles and PBC in Japan, a recent study suggested that different HLA variants may relate to clinical features of disease. Indeed, Nakamura and colleagues reported a strong association of an HLA-DRB1*0405 and DRB1*0803 with disease only in the subset of patients positive for anti-sp100 (odds ratio = 1.61), a well-known PBC-specific serum anti-nuclear autoantibody, and anticentromere antibodies (odds ratio = 2.30).70 Interestingly, Hirschfield et al. found similar data in Caucasian populations.73 Also, because of the potential clinical implication, future association studies should address the link between different HLA variants and immunological phenotypes in PBC. Overall, we can conclude that the picture of HLA class II involvement in PBC was quite complex and uninteresting until recently.
More Recent Findings: Renewed Interest in HLA.
On the basis of the above data, it is clear why until recently HLA variants did not arouse great interest of basic and clinical researchers working to characterize the molecular mechanisms that contribute to disease development, and more specifically, for understanding the role of genetics in PBC. This began to change when our group showed that beyond the consistent (but weak) positive association with HLA DRB1*08 allele, PBC was also strongly associated with two protective HLA variants, DRB1*11 and DRB1*13 (first reported in abstract form in 200512).13 In particular, by typing for HLA class II polymorphisms in a large cohort of 664 Italian patients with PBC and 1992 controls, we confirmed the known positive association with DRB1*08 (odds ratio = 3.3), whereas we reported for the first time the protective alleles DRB1*11 (odds ratio = 0.4) and DRB1*13 (odds ratio = 0.7). A weak association with HLA DRB1*02 was also found, and only the associations with DRB1*08 and DRB1*11 were common to all geographical areas of Italy (Northern, Central, and Southern Italy).13 These results were later confirmed in a large UK set of patients and controls in which protection against PBC was associated with DRB1*13 (odds ratio = 0.65) along with a positive association with the class II MHC allele DRB1*0801 (odds ratio = 3.05).14 The finding is of great interest, because the two HLA variants found to be protective for PBC suggest possible disease mechanisms as having a protective role for multiple infectious diseases. Indeed, these studies suggest that the HLA-DRB1*11 allele exerts a strong protective role against hepatitis C virus,74 human papilloma viruses,75 and human immunodeficiency virus.76 Similarly, HLA-DRB1*13 is protective for hepatitis B virus,77 hepatitis C virus,78 human papilloma viruses,79 human immunodeficiency virus,80 and malaria.79 Overall, these data indicate that these HLA class II alleles may influence the maintenance of immune tolerance as well as the penetrance of infectious agents, thus having implications in light of the proposed infectious theory in PBC etiology.1 In accordance with this, because the protective HLA alleles are associated with resistance to several infections, it can be hypothesized that the lack of such alleles might contribute to the molecular mimicry of infectious agents, leading to immune tolerance breakdown in PBC.1
Hints From GWAS: HLA Turns Out to Be the First Association with PBC.
The field of human genetics has rapidly changed since the recent completion of the human genome sequence, and novel, challenging theories have been proposed. Overall, thanks to dramatic advances in molecular technology linked to the field of genetics,81 we are now witnessing an explosion of new information about the allelic architecture of human complex diseases, such as PBC.82 In particular, the ability to evaluate the entire human genome for common polymorphisms (i.e., those present in more than 5% of the general population) has allowed us to disclose more than 80 disease-susceptibility loci. The catalog of the National Cancer Institute–National Human Genome Research Institute reports an updated list of published GWAS (http://www. genome. gov/26525384). It is of great interest that the recent GWAS approaches have allowed the identification of an extended major histocompatibility complex, spanning approximately 7.6 megabases of the human genome.83 Indeed, many additional loci (most with a putative immunoregulatory role) were identified outside the well-known HLA class I, II, and III regions.83 A growing number of studies are providing evidence of genetic complexity within the MHC region in a number of disorders.
In PBC, the first GWAS was recently performed in cases from Canada and the United States15 and reported significant associations with HLA, as well as with other non-HLA loci including IL-12A, and IL-12RB2 polymorphisms. This first study manifested a sufficient statistical power by including 536 patients with PBC and 1536 controls typed for approximately 300,000 common variants, but more solid data were soon provided by combining data sets from the Canadian–US GWAS with a separate Italian GWAS16 (Fig. 2 and Table 2). More than 610,000 common variants were examined in 457 Italian PBC cases and more than 1 million in 947 controls. When considered alone, the Italian cohort association data set achieves genome-wide significance at the HLA locus, with several other loci showing suggestive association signals (Fig. 2A,B). Analysis of the combined data set (998 cases and 8777 controls) showed many more loci to have reached the conservative genome-wide threshold P value (P < 5 × 10−8), most of these also showed P values < 5 × 10−5 in the Italian-alone cohort. In particular, this meta-analysis allowed confirmation of the finding that HLA regions had the strongest statistical association with PBC. At the HLA region, the variants showing the strongest associations with PBC were similar between the two data sets, with almost complete overlap of the strongest association observed between the DQB1 and DQA2 loci (Fig. 2B). Importantly, the association with HLA region were also confirmed and strengthened by a third GWAS, recently conducted in a very large cohort of 1840 UK PBC cases and 5163 population controls17 (Table 2).
Taken together, these three GWAS identified a number of non-HLA loci, with plausible candidate genes that indicate the involvement of the innate and adaptive immune systems in the etiopathogenesis of PBC (Table 2). In particular, these findings support the role for the Toll-like receptor, TNF, and nuclear factor kappa B (NF-κB) pathways. Among the associations consistently reported are, notably, those with the IL-12A and IL-12RB2 loci, the gene encoding the SPi-B transcription factor (SPIB), as well as two other loci, the gene encoding interferon regulatory factor 5 (IRF5) and the gene encoding the IKAROS family zinc finger 3 (IKZF3), and that encoding ORM1-like 2 (ORMDL3) also implicated in risk for other autoimmune diseases such as lupus and asthma, respectively. Suggestive associations were also observed between PBC and two other loci associated with other autoimmune conditions, the signal transducer and activator of transcription 4 (STAT4) and DENND1B. Finally, the most recent UK GWAS identified novel associations between PBC and loci, such as CD80, NF-κB1, IL-7R, CXCR5, and TNFAIP217 (Table 2). These studies clearly identified PBC association with several novel non-HLA loci and added evidence of overlaps in the risk loci predisposing to PBC and other autoimmune diseases. However, all these novel genetic data allow us to make some observations. First, a greater number of studies and of subjects (cases and controls) who are studied results in a greater number of common genetic variants associated with PBC. This suggests caution in some way and the reasonable need to redirect our future research studies, for example, to rare variants or to copy number variants or to gene expression. The second observation is the strong consistency among the findings of these three GWAS, thus suggesting the presence of a common genetic pattern for PBC. This finding is very positive, but again, caution is needed, because the first three GWAS have been performed in populations of European ancestry, and it will be important also to replicate the reported associations in non-European populations. Indeed, a recent study from Japan failed to confirm some GWAS-associated variants.84
Conclusions and Future Developments
It is currently believed the development of PBC requires that an environmental factor, particularly an infection, initiates an autoimmune reaction in a genetically predisposed individual. However, although strongly implicated by familial and twin studies, no specific genetic factors involved in susceptibility to PBC were identified. This began to change first with the demonstration of associated protective HLA variants by means of large-scale candidate-gene association studies. However, the major role of the HLA region in the genetic architecture of PBC susceptibility became definitively clear after the first GWAS in PBC. On the basis of these data, it will be challenging to perform a deep, high-throughput analysis of this genetic region, although these efforts must consider that the extensive linkage disequilibrium and variability across the HLA region makes a further resolution of these associations difficult. Moreover, because the HLA molecules are tightly linked with the maintaining (or breaking) of the immune system homeostasis, functional studies on new candidate HLA variants have to be carried out with the final goal of understanding PBC etiopathogenesis and developing novel disease-specific therapies.