255

Genetics and Epigenetics of Primary Biliary Cirrhosis Marco Carbone, MD2,3

Ana Lleo, MD, PhD1

1 Liver Unit and Center for Autoimmune Liver Diseases, Humanitas

Clinical and Research Center, Rozzano (MI), Italy 2 Division of Gastroenterology and Hepatology, Department of Medicine, Addenbrooke’s Hospital, Cambridge, United Kingdom 3 Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom 4 Division of Rheumatology, Allergy and Clinical Immunology, University of California at Davis, Davis, California

Pietro Invernizzi, MD, PhD1,4

Address for correspondence Pietro Invernizzi, MD, PhD, Liver Unit and Center for Autoimmune Liver Diseases, Humanitas Clinical and Research Center, Via A. Manzoni 56, 20089 Rozzano (MI), Italy (e-mail: [email protected]).

Semin Liver Dis 2014;34:255–264.

Abstract

Keywords

► primary biliary cirrhosis ► genome-wide association study ► sex chromosomes ► immune-related pathways ► novel drugs

Primary biliary cirrhosis (PBC) has been considered a multifactorial autoimmune disease presumably arising from a combination of environmental and genetic factors, with genetic inheritance mostly suggested by familial occurrence and high concordance rate among monozygotic twins. In the last decade, genome-wide association studies, new data on sex chromosome defects and instabilities, and initial evidence on the role of epigenetic abnormalities have strengthened the crucial importance of genetic and epigenetic factors in determining the susceptibility of PBC. High-throughput genetic studies in particular have revolutionized the search for genetic influences on PBC and have the potential to be translated into clinical and therapeutic applications, although more biological knowledge on candidate genes is now needed. In this review, these recent discoveries will be critically summarized with particular focus on the possible steps that may transfer genetic and epigenetic knowledge to direct health benefits in patients with PBC.

Primary biliary cirrhosis (PBC) is considered a paradigmatic model of organ-specific autoimmune diseases characterized by loss of tolerance, production of a multilineage immune response to mitochondrial and nuclear proteins, inflammation and progressive destruction of intermediate intrahepatic small ducts leading in some patients to fibrosis, cirrhosis, and ultimately liver transplantation or death.1–3 Primary biliary cirrhosis is a rare disease with population-based studies indicating a wide range in yearly incidence (0.33–5.8/ 100,000) and point prevalence (1.91–40.2/100,000) rates.3 The recent development of animal models of PBC allows for the elucidation of many aspects of the pathogenesis of this autoimmune disease,4,5 including rigorous definitions of the serum signatures of antimitochondrial antibodies (AMAs) and disease-specific antinuclear autoantibodies (ANAs), as well as the definition of autoreactive T-cell responses and their asso-

Issue Theme Primary Biliary Cirrhosis; Guest Editor, Pietro Invernizzi, MD, PhD

ciation with some immunological signaling pathways, such as tumor necrosis factor (TNF) and nuclear factor kappa-lightchain-enhancer of activated B cells (NF-κB). The autoimmune nature of PBC also suggests a striking female predominance; epidemiological data indicate that family members of patients have an increased risk of developing PBC or other autoimmune disorders. Primary biliary cirrhosis can be diagnosed with confidence in patients with an otherwise unexplained elevation of alkaline phosphatase and gamma-glutamyl transferase and presence of AMAs and PBC-specific ANAs. A liver biopsy is not essential for the diagnosis of PBC, but is recommended because it allows one to assess the activity and stage of the disease.6 The only approved therapy for PBC is ursodeoxycholic acid (UDCA), an hydrophobic bile acid with protective effects on injured cholangiocytes mainly due to its ability to induce ductular alkaline choleresis.

Copyright © 2014 by Thieme Medical Publishers, Inc., 333 Seventh Avenue, New York, NY 10001, USA. Tel: +1(212) 584-4662.

DOI http://dx.doi.org/ 10.1055/s-0034-1383725. ISSN 0272-8087.

This document was downloaded for personal use only. Unauthorized distribution is strictly prohibited.

Ilaria Bianchi, MD, PhD1

Genetics and Epigenetics of Primary Biliary Cirrhosis

Bianchi et al.

Although familial occurrence and monozygotic twins’ concordance have suggested a strong heritability in PBC, no specific candidate genes have been identified. For decades, the only exception was a weak association with the DRB1
08 allele, a class II human leukocyte antigen (HLA), and two additional protective associations with the HLA DRB1
11 and DRB1
13 alleles.7–9 In the last few years, interest in HLA genes has grown significantly10 thanks to the genome-wide association studies (GWASs) and illumina immunoarray- (immunochip) association studies which demonstrated that the major component of the genetic architecture of this disease are within the HLA region.11–16 Unfortunately, the reasons why specific HLA alleles increase or reduce the risk for PBC development remains unclear.

Similar to many genetically complex diseases, such as rheumatoid arthritis, multiple sclerosis, and Crohn disease, recent high-throughput genetic studies in PBC have also identified dozens of novel disease-associated non-HLA variants.11–16 Overall, the non-HLA risk alleles were found in conjunction with genes related to immune functions (►Table 1), with important contributions from several immune pathways—these latter ranging from the antigen presentation and T-cell differentiation (class II HLA, IL12, IL12R, IL7R, CD80, STAT4, TYK2, SOCS1), the differentiation of myeloid cell lineage (IRF5, IRF8, SPIB, and IL-7R), to the B-cell function (SPIB, PLC-L2, IRF8, PLC-L2, CXCR5, IKZF3).17,18 These genetic variants are not specifically involved in one unique function.

Table 1 Nonhuman leukocyte antigen risk loci identified in at least one high-throughput genetic study of primary biliary cirrhosis (PBC) Locus

SNP

Odds ratio

P value

Candidate gene

Diseases sharing risk loci with PBC

Referencesa

1p36

rs3748816

1.33

3.15E-08

MMEL1

—

119

1p31.3

rs72678531

1.61

2.47E-38

IL12RB2

—

120

1q31.3

rs2488393

1.28

4.29E-12

DENND1B

CD

120

2q32.2

rs3024921

1.62

2.59E-18

STAT4

CeD, RA, T1DM, SLE, SSc

120

3p24.3

rs1372072

1.2

2.28E-08

PLCL2

MS

120

3q13.3

rs2293370

1.39

6.84E-16

CD80

MS, CeD, Vit

120

3q25.33

rs2366643

1.35

3.92E-22

IL12A

MS, CeD

120

4q24

rs7665090

1.26

8.48E-14

NFKB1

MS, UC

120

5p13

rs6871748

1.3

2.26E-13

IL7R

MS, UC

120

7p14.1

rs6974491

1.57

4.44E-08

ELMO1

MS, CeD, PS

120

7q32

rs35188261

1.52

6.52E-22

IRF5

UC, RA, SLE, SSc,

120

9q32

rs4979462

1.57

1.85E-14

TNFSF15

UC, CD

14

11q13

rs538147

1.23

2.06E-10

RPS6KA4

MS, CD, PS, SARC

13

11q23.3

rs80065107

1.39

7.20E-16

CXCR5

MS, CeD, SLE, VIT

120

11q23

rs4938534

1.38

3.27E-08

POU2AF1

CeD

120

12p13.2

rs1800693

1.27

1.18E-14

TNFRSF1A

MS

120

12q24

rs11065979

1.2

2.87E-09

SH2B3

CeD, RA, T1DM, VIT, PSC

120

13q14

rs3862738

1.33

2.18E-08

TNFSF11

CD

13

14q24

rs911263

1.26

9.95E-11

RAD51B

—

120

14q32

rs8017161

1.22

2.61E-13

TNFAIP2

—

13

16p13.13

rs12708715

1.29

2.19E-13

CLEC16A

MS, UC, T1DM

120

16q24.1

rs11117433

1.26

1.41E-09

IRF8

MS, UC, RA, SSc

120

17q12

rs17564829

1.26

6.05E-14

IKZF3

UC, CD, RA, T1DM

120

17q21.1

rs17564829

1.25

2.15E-09

CRHR1

—

120

19p13.2

rs34536443

1.91

1.23E-12

TYK2

MS, CD, RA, SLE, PS

120

19q13.3

rs3745516

1.46

7.97E-11

SPIB

—

120

22q13.1

rs2267407

1.29

1.29E-13

MAP3K7IP1

CD

120

Abbreviations: CD, Crohn disease; CeD, celiac disease; MS, multiple sclerosis; PS, psoriasis; RA, rheumatoid arthritis; SARC, sarcoidosis; SNP, singlenucleotide polymorphism; SLE, systemic lupus erythematosus; SSc, systemic sclerosis; T1DM, diabetes mellitus type 1; UC, ulcerative colitis; VIT, vitiligo. a For each locus, results are from the study with strongest evidence of association. Seminars in Liver Disease

Vol. 34

No. 3/2014

This document was downloaded for personal use only. Unauthorized distribution is strictly prohibited.

256

Genetic factors in PBC are further suggested by a strong female preponderance and a higher risk for disease development in female relatives of PBC patients.19–30 It has been suggested that this may be at least partially related to sex chromosome defects because many genes involved in immunological tolerance are located on the X chromosome.30–35 Although high-throughput genetic studies seem to exclude the presence of genetic aberrancies of the X chromosome in PBC, some recent data are disclosing a role for epigenetic modifications of the regulatory mechanisms of specific Xlinked genes.36,37 Epigenetic modifications such as DNA methylation may explain the environmental influence on individual susceptibility to PBC; further studies are needed to fully understand their role in the pathogenesis and female preponderance of PBC.38 In this review, we will mainly focus on the recent progress obtained with high-throughput genetic studies and studies of sex chromosomes and epigenetic abnormalities, and on how these data may transform the landscape of PBC research as well as our daily clinical practice with PBC patients.

Highlights from High-Throughput Genetic Studies The advent of genome-wide association technology has changed the landscape of genetics research in PBC, as well as in many other complex diseases, such as inflammatory bowel disease39 and diabetes.40 Genome-wide association studies allows for the identification of common genetic variants in a nonbiased fashion, based on the assumption that at least part of the genetic factors in many common diseases are attributable to a small number of common allelic variants present in more than 5% of the general population.41 These studies generally analyze millions of common genetic variants in both known and unknown genes or regulatory regions, require a large sample size to avoid false-positive findings and because of the low effect size of most disease variants (odds ratios ¼ 1.1–1.4),42 and have to include a replication of strongest associations in independent casecontrol panels. Large and well-characterized patient cohorts for genetic studies of PBC have been recently established in Europe, North America, and Japan, and four GWAS11–14 and two iCHIP-association studies15,16 revealed dozens of PBC-associated loci (►Table 1). These studies have provided important insights into the allelic architecture of PBC, and have shown that most of these genetic variants are not specifically involved in one unique function, but play an important role in several different immune pathways. For instance, IL-7R has a role in myeloid cell differentiation,43 but it also controls thymic CD8-lineage specification and peripheral naive Tcell homeostasis; it is also involved in the induction of Tcell activation.44 These studies also highlighted the considerable overlap of genetic susceptibility factors between PBC and several clinically associated autoimmune disorders. The identification of candidate genes at pleiotropic loci suggests that common pathways are involved in the pathogenesis of PBC as of other clinically associated disorders. These observations

Bianchi et al.

suggest that although distinct mechanisms might predispose to a particular phenotype/disease, there are unique immunologic pathways underling autoimmunity that should be targeted with novel drugs. Finally, as one of the major goals of high-throughput genetic studies is the identification of key pathways implicated in the pathogenesis of PBC, these studies could help to reveal novel therapeutic targets for this liver disease. Indeed, in PBC there is still a gap between our basic knowledge of the disease and novel therapeutic approaches. Ursodeoxycholic acid has been the only drug approved for PBC in the last two decades; however, a large number of new biologics merit further investigation in this disease to show their safety and efficacy.45 This is especially important because up to 40% of PBC patients do not respond to UDCA.1 Some of the pathways that may have therapeutic implications in PBC are reported below and are listed in ►Table 2.

Nuclear Factor Kappa-Light-Chain-Enhancer of Activated B Cells Loci containing genes involved in activation of NF-κB were identified by two GWASs in PBC13,14; in particular, the NFKB1 gene itself and genes in the NF-κB activation pathways such as CD80, TNFRSF1A, and RPS6KA4. Nuclear factor kappa-lightchain-enhancer of activated B cells is a well-known transcription factor able to regulate expression of a large number of genes involved in the immune response. Interestingly, NF-κB is highly activated in many other autoimmune disorders such as rheumatoid arthritis and asthma.46 Growing evidence indicates that coinhibitory molecules, such as CD80, have a key protective role in autoimmunity. One of the most largely characterized inhibitory pathways for the activation of T cells is the CD80/CD86:CD28/CTLA-4 (cytotoxic T lymphocyte-associated antigen 4) pathway.47,48 CD28 is a cell-surface protein constitutively expressed on both naïve and activated T lymphocytes; CD80 and CD86 are expressed on antigen-presenting cells. However, CD80 is little expressed on resting antigen-presenting cells and is upregulated only with prolonged interaction with T cells, whereas CD86 is constitutively expressed and can be rapidly upregulated on antigen-presenting cells. For this reason, CD86 is mainly involved in rapid and initial T-cell activation, whereas CD80 plays a key role in maintaining immune responses to chronic inflammation. The activation of T lymphocytes upregulates the expression of CTLA-4 (CD152), with consequent negative signal and inhibition and termination of T-cell responses. With the aim of new drug development, a fusion protein expressing the extracellular domain of CTLA-4 and the constant region of IgG has been created to block the interaction between CD28 and CD80-CD86; because CTLA-4 binds CD86 and CD80 with much higher affinity than CD28 does,34 it is expected that this fusion protein would mostly inhibit T cells that respond to self-antigens without affecting resting lymphocytes that recognize other antigens. The efficacy of this CTLA-4 Ig (abatacept) has already been preclinically evaluated with encouraging results in several animal models, including PBC models.49 After these early in vivo studies, abatacept was demonstrated to be effective in a broad spectrum of Seminars in Liver Disease

Vol. 34

No. 3/2014

257

This document was downloaded for personal use only. Unauthorized distribution is strictly prohibited.

Genetics and Epigenetics of Primary Biliary Cirrhosis

Genetics and Epigenetics of Primary Biliary Cirrhosis

Bianchi et al.

Table 2 Molecular pathways identified in high-throughput genetic studies of primary biliary cirrhosis Pathways

Mechanisms

Drugs

Diseases in which inhibitors of these pathways have been evaluated

NF-κB

NF-κB regulates the expression of many genes involved in the immune response. NF-κB coinhibitory molecules are important in loss of tolerance. The CD80/CD86-CTLA-4 pathway is a key inhibitory pathway for activation of T cells

Anti-CD80 (abatacept)

Psoriasis52 Rheumatoid arthritis50,51

IL-12/IL-23

IL-12 stimulates the Th1-type immune response, thus contributing to loss of tolerance in many models of autoimmunity; IL-23 is essential for the differentiation of Th17 cells

Anti-IL-12/IL-23 (ustekinumab)

Crohn disease58,59 Psoriasis60

Hedgehog signaling

Key pathway in the response to cholestatic damage

Hedgehog-inhibitor (cyclopamine)

Psoriasis121

Phosphatidylinositol signaling

Crucial pathway for self-tolerance maintenance

__

TNF-α

Recent evidence indicates a dualistic, immunosuppressive and proinflammatory role for TNF in autoimmune conditions

Anti-TNF (infliximab, golimumab, etanercept, adalimumab, certolizumab)

__ Rheumatoid arthritis122 Ankylosing spondylitis123 Psoriasis124 Crohn disease125

Abbreviations: IL, interleukin; NF-κB, nuclear factor kappa-light-chain-enhancer of activated B cells; TNF, tumor necrosis factor.

patients with rheumatoid arthritis from early stage to refractory diseases who are resistant to other therapies such as TNF blockers50,51 and in a phase I trial in patients with psoriasis.52 To block the costimulation between T lymphocytes and antigen-presenting cells through CD80 is clearly an important therapeutic approach for the treatment of PBC with incomplete UDCA response.

Interleukin 12 (IL-12)/IL-23 T-cell differentiation is another pathway suggested to have a role in the development of the disease by loci identified in GWAS. Th1 immune responses have been implicated in the underlying pathogenic mechanisms of most autoimmune diseases53 and are clearly involved in the development of autoreactive T cells. This is consistent with the role of the pyruvate dehydrogenase complex-specific autoreactive Th1 cells in the immunopathogenesis of PBC.54 It is known that anti-interleukin-12 (IL-12) signaling together with the IL-12 driven interferon-γ production, promotes Th1 immune response and loss of tolerance by differentiating naïve T cells to Th1 lymphocytes.55 Genome-wide association studies of PBC disclosed three loci containing genes involved in IL-12 signaling: the signal transducer and activator of the transcription (STAT4) gene13 and the genes IL12A, IL12RB211–13 codifying the subunit p35 of the IL-12, and the chain IL12Rβ2 of the IL-12 receptor, respectively.56 Studies conducted in an animal model of PBC by Gershwin’s group have clearly showed a role for the IL-12 pathway in this disease.57 Seminars in Liver Disease

Vol. 34

No. 3/2014

Several monoclonal antibody and inhibitors of p40, a subunit of the IL-12 receptor, have been developed and multiple clinical trials have shown therapeutic benefit in Crohn disease58,59 and psoriasis.60 The differentiation of Th17 cells involves not only the p40 subunit of IL-12 receptor, but also a component of the dimeric cytokine IL-23; pilot studies are under way to test the safety and efficacy of the human monoclonal anti-IL-12/IL-23 in PBC patients (ClinicalTrials. gov identifier: NCT01389973). Nevertheless, several questions remain and additional studies are needed. In particular, we need to clarify the crosstalk between IL-12 and IL-23 signaling pathways to better define the specific IL12A and IL12RB2 alleles conferring risk for PBC by means of further genetic association studies and sequencing studies, and to elucidate the relative contributions of Th17, Treg cells, and other immunocellular subpopulations to PBC by in vivo experiments. Finally, specific studies should be performed to understand the role for IL-35 because the cytokine IL-35 and its receptor include IL-12 p35 and IL-12Rβ2 among their subunits. The final goals of these studies should be to develop a novel therapy with a better outcome for patients with PBC.

Phosphatidylinositol Signaling and Hedgehog Signaling Pathways The phosphatidylinositol signaling system pathway is a key component of the adaptive immune response and is essential to maintaining self-tolerance as it is known to mediate the

This document was downloaded for personal use only. Unauthorized distribution is strictly prohibited.

258

effects of TNF-α on NF-kB activation.61–63 Pathway analysis of the Canadian and Italian GWAS PBC cohorts have highlighted the possible involvement of this pathway in PBC, thus supporting the TNF hypothesis.61,62 This same study also suggested the involvement in the genetic architecture of PBC of the hedgehog (Hh) signaling system, a group of secreted proteins with a role in adult stem cell proliferation and organogenesis.64–66 Hh signaling has been widely characterized in PBC. In PBC, Hh signaling has been described as involved in the ductular response to cholestasis, characterized by proliferation of cholangiocytes and myofibroblastic cells.67 Hh signaling was found to promote the survival of biliary epithelial cells68 its activation is associated with increased ductular cell expression of proinflammatory genes, such as the gene producing Cxcl16, and in chemotaxis of the natural killer (NK) T cell toward cholangiocytes.69 Although preliminary, these data show that Hh signaling promotes the survival of potential hepatic progenitor cells and indicate that it is an important protective factor within the inflamed and damaged liver. The Hh signaling pathway may well represent a novel therapeutic target to promote cell proliferation and tissue repair in PBC and possibly other chronic liver diseases.

Tumor Necrosis Factor-α Tumor necrosis factor-α is known to play an important role in liver homeostasis by activating several intracellular pathways that determine the fate of hepatocytes.70 In particular, the TNF-α pathway is largely involved in the induction of apoptosis and activation of NF-kB signaling, which is proinflammatory and antiapoptotic.71 In PBC, GWASs identified several loci-containing genes in TNF-α signaling pathways such as TNFAIP2,13,14 TNFRSF1A, and DENND1B.13 Interestingly, DENND1B interacts directly with TNFRSF1A, one of two receptors for TNF-α,72 and was found to be associated with asthma.73 Knockout mice for the TNFRSF1A gene show milder liver fibrosis when compared with wild-type mice treated with a potent chemical that induces liver injury.74 We have shown that macrophages from PBC patients produce TNF-α when stimulated with apoptotic bodies from cholangiocytes and serum AMA.75 In addition, serum levels of TNF-α correlate with disease stage in PBC.76 Finally, the pathway analysis of the Italian GWAS cohort identified the TNF signaling pathway by applying a “self-contained” GWAS pathway analysis method (the linear combination test [LCT]).17 All these findings clearly indicate a key role for TNF-α in the pathogenesis of PBC and suggest the use of anti-TNF-α agents, currently accepted drugs for several autoimmune and inflammatory diseases, for the treatment of PBC.

The Genetics of Sex Chromosomes Primary biliary cirrhosis is characterized by a female preponderance and a higher risk for disease development in female relatives of patients with PBC, but the reason is still unclear. Links between the X chromosome and immunity have been strengthened by clinical data, such as X-linked immunodeficiencies,77 and the presence of many autoimmune features

Bianchi et al.

and autoimmune diseases in patients with Turner syndrome.78 In the last decade, several major defects in sex chromosomes of patients with PBC were reported.31,32,79–81 Our group evaluated the frequency of X monosomy by fluorescence in situ hybridization of peripheral leukocytes in 100 female patients with PBC, 50 patients with chronic hepatitis C, and 50 healthy women and showed that women with PBC have an enhanced frequency of monosomy X compared with controls31 and that the frequency of monosomy X increased with age. This major genetic defect may contribute to the explanation of why PBC occurs predominantly in middle-aged women and is absent in the pediatric age.82–85 We also noted that X monosomy was a feature of systemic sclerosis and autoimmune thyroid disease, which are often found to be concomitant in PBC patients,32 but not of other autoimmune disease such as systemic lupus erithematosus.33 Our group also showed that X monosomy was more frequent in peripheral T and B lymphocytes than blood cells from the innate immune system such as monocytes and NK cells.31,32 Importantly, these findings were confirmed by others in Reynold syndrome, a laminopathy with combined PBC and progressive systemic sclerosis (SSc).86 In particular, X monosomy was found in 12% of patients with Reynold syndrome, 10% in PBC, 9% in SSc, and 6% in age-matched healthy controls.86 X-chromosome defects are more frequent in women with late-onset autoimmune disease.31,32,87 In PBC not only X-chromosome loss occurred more frequently but in a preferential fashion,88 further supporting the critical involvement of X-chromosome gene products in the disease and its female preponderance. It is still unknown the origin of the remaining X chromosome, as imprinting may also play a role in PBC development.88 In a more recent study, we also demonstrated that Ychromosome loss is higher in PBC males compared with healthy male controls, and that this phenomenon increases with aging.35 This confirms the existence of an analogous mechanism in the male population to previously identified X haploinsufficiency in female patients with organ-specific autoimmune disease. It is possible that the Y chromosome loss causes an imbalance for the alleles shared with X chromosomes as well as the loss of one X chromosome might lead to the haploinsufficiency of X-linked loci, thus escaping X-chromosome inactivation processes. The role of the Y chromosome in immunology and specifically in autoimmunity is still debated, but because a similar major genetic defect was found in male with autoimmune thyroiditis,89 it is possible that this commonality might represent a relevant feature in the etiopathogenesis of autoimmune diseases that should be further investigated. The Y chromosome does not contain vital genes because females do not have it. In particular, the Y chromosome harbors a limited number of Xchromosome homologues, mainly located at the pseudoautosomal regions, potentially relevant for the immune function.90 Among others, the interleukin receptors IL3RA and IL9R are possible candidates. IL3 might be implicated in the intracellular interaction between STAT5 molecules and PDCE2, the autoantigen in PBC,91 whereas imbalances of IL9R might have an effect on the suppressive T-cell compartment, Seminars in Liver Disease

Vol. 34

No. 3/2014

259

This document was downloaded for personal use only. Unauthorized distribution is strictly prohibited.

Genetics and Epigenetics of Primary Biliary Cirrhosis

Genetics and Epigenetics of Primary Biliary Cirrhosis

Bianchi et al.

being expressed by T cells.92 Another Y-chromosome gene that might be implicated in PBC pathogenesis and autoimmunity is the Y-linked autoimmune acceleration (Yaa)93 because the Yaa translocation from the telomeric end of the X chromosome onto the Y chromosome94 is known to cause this gene overexpression,95 and a consequent Yaa-mediated acceleration of lupus-like disease.96 Based on these data, it is possible that translocation of other X-linked genes to the Y chromosome mighty contribute to the initiation and perpetuation of PBC and autoimmunity.

Epigenetic Abnormalities in Primary Biliary Cirrhosis Epigenetics include any heritable and functional relevant changes in gene activity that are not caused by changes in the nucleotide sequence. There are several types of epigenetic mechanisms, although only four are generally accepted to be examples of epigenetics: (1) posttranslational modifications of the amino acids that make up histone tails of nucleosomes (i.e., methylation, acetylation, ubiquitination, etc.), (2) addition of methyl groups to the DNA to convert certain cytosine residues to 5-methylcytosine, (3) remodeling of chromatin by complexes of proteins that can enhance or suppress gene expression, and (4) silencing of gene expression by small noncoding RNA transcripts such as microRNA.97 The role of epigenetics in loss of tolerance and in the pathogenesis of rheumatic and autoimmune diseases, such as systemic lupus erythematosus, has been extensively described.98–102 Based on much evidence, it has been suggested that the lack of concordance in monozygotic twins in autoimmune diseases indicates that epigenetic factors are important in determining the susceptibility to autoimmunity besides environmental factors.81,103,104 On the contrary, in PBC only few studies are available on epigenetic factors,99 but these scanty data are disclosing a key role of epigenetic abnormalities in the disease.36,88,105 The studies on epigenetic abnormalities in PBC started about 10 years ago and focused on X chromosomes. Indeed, women are functional mosaics for X-linked genes and most genes on one of their two X chromosomes are silenced by mean of a DNA methylation process leading to an X-chromosome inactivation (XCI), although up to 15% of genes can escape XCI. This process is necessary to achieve equivalent dosage of X-linked gene products between males and females.106 In addition, it has been shown that up to 10% of total X-linked genes manifest variable XCI patterns in different individuals.106 Interestingly, it has been shown that women affected with several autoimmune diseases that are concomitant with PBC, such as SSc, autoimmune thyroid diseases, and Sjögren syndrome, manifest a skewed X inactivation in their peripheral blood cells.107–110 For these reasons, we set out to determine the mechanism of XCI in 166 female PBC patients and 266 age-matched controls, consisting of both healthy subjects and patients with liver disease, but we failed to find a preferential inactivation in PBC.88 It should be noted, however, that only this latter study accounted for more than one locus, whereas previous reports only investigated the androgen receptor methylation that poorly represents XCI. Seminars in Liver Disease

Vol. 34

No. 3/2014

More recently, Mitchell et al36 analyzed 125 variable Xchromosome inactivation status genes in peripheral blood mRNA and DNA from monozygotic discordant and concordant pairs. Consistently downregulated genes included CLIC2 and PIN4 in the twin with PBC, which was not found in the healthy twin or in control subjects.36 These data suggest that the possible mechanisms by which epigenetic factors influence PBC onset are likely much more complex than a simple X-linking of candidate genes.3,35,36,81 The interaction of CD40 and CD40L plays a key role in CD4þ T-cell priming, B-cell terminal maturation, and immunoglobulin class-switch recombination. Genetic defects in the CD40L gene, a gene located on the X chromosome, cause an immunodeficiency with elevated serum IgM levels.77 No gene mutations were detected in cDNA of CD40L from PBC patients by reverse-transcription polymerase chain reaction singlestrand conformation polymorphism (RT-PCR-SSCP) technique.111 Lleo et al have recently demonstrated significantly lower levels of DNA methylation of the CD40L promoter in CD4 þ T cells from PBC patients compared with controls, and more importantly, a decreased methylation inversely correlated with levels of serum IgM in PBC patients.37 The finding of a decreased DNA methylation of the CD40L promoter together with the absence of genetic defects of the CD40L gene in patients with PBC strongly suggests that environmental factors rather than genetics play a key role in the pathogenesis of elevated serum IgM in PBC. Other candidate immune-related genes of the X chromosome might have similar epigenetic defects in PBC and should be investigated in future studies. For example, the Foxp3 gene, which localizes in the short arm of the X chromosome, is important for T cells with regulatory functions; its deficiency leads to a highly aggressive and often fatal multiorgan autoimmune disease.112 Abnormalities in microRNAs expression are another epigenetic factor recently evaluated in PBC. MicroRNAs are known to play a vital role in the regulation of various aspects of immune function and in the development of autoimmune disease. It has been first shown that PBC is associated with altered expression of 35 hepatic microRNAs.113 In a subsequent study, 17 microRNAs are differentially expressed in peripheral blood mononuclear cells from patients with PBC.114 Although other microRNAs, such as miR-506, miR2, miR-let-7b, miR-505–3p, and miR-197–3p, were found to be associated with PBC,115–118 the precise role of microRNA in PBC remains unclear.

Conclusion Current evidence suggests a prominent role for genetic and epigenetic abnormalities in the development of PBC. With the application of genome-wide technology, HLA was confirmed as the strongest association in PBC and many other risk loci have been identified, including IL12A, IL12RB2, IRF5-TNPO3, STAT4, MMEL1, SPIB, 17q12.21, and CTLA-4. High throughput efforts to sequence exomes and genomes and the advent of deep sequencing have identified several pathways (i.e., TNF signaling, apoptosis, and antigen processing and

This document was downloaded for personal use only. Unauthorized distribution is strictly prohibited.

260

Genetics and Epigenetics of Primary Biliary Cirrhosis

Acknowledgments MC is supported in part by the Dame Sheila Sherlock EASL Fellowship Program of the European Association for the Study of the Liver (EASL). AL and PI are supported in part by the National Institutes of Health (NIH) grant #DK091823– 01A1.

13 Mells GF, Floyd JA, Morley KI, et al; UK PBC Consortium; Wellcome

14

15

16

17

18

19 20

21

References

22

1 Invernizzi P, Selmi C, Gershwin ME. Update on primary biliary

cirrhosis. Dig Liver Dis 2010;42(6):401–408 2 Lleo A, Invernizzi P. Apotopes and innate immune system: novel

3

4

5

6

7

8

9

10 11

12

players in the primary biliary cirrhosis scenario. Dig Liver Dis 2013;45(8):630–636 Podda M, Selmi C, Lleo A, Moroni L, Invernizzi P. The limitations and hidden gems of the epidemiology of primary biliary cirrhosis. J Autoimmun 2013;46:81–87 Tsuda M, Zhang W, Yang GX, et al. Deletion of interleukin (IL)12p35 induces liver fibrosis in dominant-negative TGFβ receptor type II mice. Hepatology 2013;57(2):806–816 Ando Y, Yang GX, Tsuda M, et al. The immunobiology of colitis and cholangitis in interleukin-23p19 and interleukin-17A deleted dominant negative form of transforming growth factor beta receptor type II mice. Hepatology 2012;56(4):1418–1426 European Association for the Study of the Liver. EASL Clinical Practice Guidelines: management of cholestatic liver diseases. J Hepatol 2009;51(2):237–267 Invernizzi P, Battezzati PM, Crosignani A, et al. Peculiar HLA polymorphisms in Italian patients with primary biliary cirrhosis. J Hepatol 2003;38(4):401–406 Invernizzi P, Selmi C, Poli F, et al; Italian PBC Genetic Study Group. Human leukocyte antigen polymorphisms in Italian primary biliary cirrhosis: a multicenter study of 664 patients and 1992 healthy controls. Hepatology 2008;48(6):1906–1912 Donaldson PT, Baragiotta A, Heneghan MA, et al. HLA class II alleles, genotypes, haplotypes, and amino acids in primary biliary cirrhosis: a large-scale study. Hepatology 2006;44(3):667–674 Invernizzi P. Human leukocyte antigen in primary biliary cirrhosis: an old story now reviving. Hepatology 2011;54(2):714–723 Hirschfield GM, Liu X, Xu C, et al. Primary biliary cirrhosis associated with HLA, IL12A, and IL12RB2 variants. N Engl J Med 2009;360(24):2544–2555 Liu X, Invernizzi P, Lu Y, et al. Genome-wide meta-analyses identify three loci associated with primary biliary cirrhosis. Nat Genet 2010;42(8):658–660

261

23

24

25

26 27

28 29

30

31

32

33

34

Trust Case Control Consortium 3. Genome-wide association study identifies 12 new susceptibility loci for primary biliary cirrhosis. Nat Genet 2011;43(11):1164 Nakamura M, Nishida N, Kawashima M, et al. Genome-wide association study identifies TNFSF15 and POU2AF1 as susceptibility loci for primary biliary cirrhosis in the Japanese population. Am J Hum Genet 2012;91(4):721–728 Juran BD, Hirschfield GM, Invernizzi P, et al; Italian PBC Genetics Study Group. Immunochip analyses identify a novel risk locus for primary biliary cirrhosis at 13q14, multiple independent associations at four established risk loci and epistasis between 1p31 and 7q32 risk variants. Hum Mol Genet 2012;21(23):5209–5221 Liu JZ, Almarri MA, Gaffney DJ, et al; UK Primary Biliary Cirrhosis (PBC) Consortium; Wellcome Trust Case Control Consortium 3. Dense fine-mapping study identifies new susceptibility loci for primary biliary cirrhosis. Nat Genet 2012;44(10):1137–1141 Kar SP, Seldin MF, Chen W, et al; Italian PBC Genetics Study Group. Pathway-based analysis of primary biliary cirrhosis genomewide association studies. Genes Immun 2013;14(3):179–186 Carbone M, Lleo A, Sandford RN, Invernizzi P. Implications of genome-wide association studies in novel therapeutics in primary biliary cirrhosis. Eur J Immunol 2014;44(4):945–954 Bach N, Schaffner F. Familial primary biliary cirrhosis. J Hepatol 1994;20(6):698–701 Brind AM, Bray GP, Portmann BC, Williams R. Prevalence and pattern of familial disease in primary biliary cirrhosis. Gut 1995; 36(4):615–617 Fagan E, Williams R, Cox S. Primary biliary cirrhosis in mother and daughter. BMJ 1977;2(6096):1195 Floreani A, Naccarato R, Chiaramonte M. Prevalence of familial disease in primary biliary cirrhosis in Italy. J Hepatol 1997;26(3): 737–738 Jaup BH, Zettergren LS. Familial occurrence of primary biliary cirrhosis associated with hypergammaglobulinemia in descendants: a family study. Gastroenterology 1980;78(3):549–555 Jones DE, Watt FE, Metcalf JV, Bassendine MF, James OF. Familial primary biliary cirrhosis reassessed: a geographically-based population study. J Hepatol 1999;30(3):402–407 Lazaridis KN, Juran BD, Boe GM, et al. Increased prevalence of antimitochondrial antibodies in first-degree relatives of patients with primary biliary cirrhosis. Hepatology 2007;46(3):785–792 Tsuji K, Watanabe Y, Van De Water J, et al. Familial primary biliary cirrhosis in Hiroshima. J Autoimmun 1999;13(1):171–178 Invernizzi P, Selmi C, Mackay IR, Podda M, Gershwin ME. From bases to basis: linking genetics to causation in primary biliary cirrhosis. Clin Gastroenterol Hepatol 2005;3(5):401–410 Invernizzi P. Role of X chromosome defects in primary biliary cirrhosis. Hepatol Res 2007;37(3, Suppl 3):S384–S388 Milkiewicz P, Heathcote J. Primary biliary cirrhosis in a patient with Turner syndrome. Can J Gastroenterol 2005;19(10): 631–633 Invernizzi P, Pasini S, Selmi C, Gershwin ME, Podda M. Female predominance and X chromosome defects in autoimmune diseases. J Autoimmun 2009;33(1):12–16 Invernizzi P, Miozzo M, Battezzati PM, et al. Frequency of monosomy X in women with primary biliary cirrhosis. Lancet 2004; 363(9408):533–535 Invernizzi P, Miozzo M, Selmi C, et al. X chromosome monosomy: a common mechanism for autoimmune diseases. J Immunol 2005;175(1):575–578 Invernizzi P, Miozzo M, Oertelt-Prigione S, et al. X monosomy in female systemic lupus erythematosus. Ann N Y Acad Sci 2007; 1110:84–91 Bianchi I, Lleo A, Gershwin ME, Invernizzi P. The X chromosome and immune associated genes. J Autoimmun 2012;38(2-3): J187–J192

Seminars in Liver Disease

Vol. 34

No. 3/2014

This document was downloaded for personal use only. Unauthorized distribution is strictly prohibited.

presentation) that might contribute to the genetic predisposition to PBC. In addition, major sex chromosome defects and loss of epigenetic controls are also disclosing mechanisms underlying the PBC susceptibility alternative to DNA defects. However, it remains unclear the real effects of these epigenetic and genetic abnormalities in PBC; additional studies are still needed to clarify the involved effector mechanisms. Dedicated studies are needed to understand the precise relationship between genetic and epigenetic risk factors and therapy response, clinical progression, and symptoms. To translate this knowledge into direct benefits for PBC patients (mainly the development of rational, disease-specific, novel therapies) will require interaction among different biomedical disciplines, including molecular biology, genomics, clinical medicine, bioinformatics, and pharmacology.

Bianchi et al.

Genetics and Epigenetics of Primary Biliary Cirrhosis

Bianchi et al.

35 Lleo A, Oertelt-Prigione S, Bianchi I, et al. Y chromosome loss in

56 Lleo A, Gershwin ME, Mantovani A, Invernizzi P. Towards com-

male patients with primary biliary cirrhosis. J Autoimmun 2013; 41:87–91 Mitchell MM, Lleo A, Zammataro L, et al. Epigenetic investigation of variably X chromosome inactivated genes in monozygotic female twins discordant for primary biliary cirrhosis. Epigenetics 2011;6(1):95–102 Lleo A, Liao J, Invernizzi P, et al. Immunoglobulin M levels inversely correlate with CD40 ligand promoter methylation in patients with primary biliary cirrhosis. Hepatology 2012;55(1): 153–160 Hewagama A, Richardson B. The genetics and epigenetics of autoimmune diseases. J Autoimmun 2009;33(1):3–11 Duerr RH, Taylor KD, Brant SR, et al. A genome-wide association study identifies IL23R as an inflammatory bowel disease gene. Science 2006;314(5804):1461–1463 Sladek R, Rocheleau G, Rung J, et al. A genome-wide association study identifies novel risk loci for type 2 diabetes. Nature 2007; 445(7130):881–885 Collins FS, Guyer MS, Charkravarti A. Variations on a theme: cataloging human DNA sequence variation. Science 1997; 278(5343):1580–1581 Hindorff LA, Sethupathy P, Junkins HA, et al. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci U S A 2009;106(23): 9362–9367 McKay FC, Hoe E, Parnell G, et al. IL7Rα expression and upregulation by IFNβ in dendritic cell subsets is haplotype-dependent. PLoS ONE 2013;8(10):e77508 Ouyang W, Oh SA, Ma Q, Bivona MR, Zhu J, Li MO. TGF-β cytokine signaling promotes CD8þ T cell development and low-affinity CD4þ T cell homeostasis by regulation of interleukin-7 receptor α expression. Immunity 2013;39(2):335–346 Tsuda M, Moritoki Y, Lian ZX, et al. Biochemical and immunologic effects of rituximab in patients with primary biliary cirrhosis and an incomplete response to ursodeoxycholic acid. Hepatology 2012;55(2):512–521 Li Q, Verma IM. NF-kappaB regulation in the immune system. Nat Rev Immunol 2002;2(10):725–734 Greenwald RJ, Freeman GJ, Sharpe AH. The B7 family revisited. Annu Rev Immunol 2005;23:515–548 Scalapino KJ, Daikh DI. CTLA-4: a key regulatory point in the control of autoimmune disease. Immunol Rev 2008;223:143–155 Dhirapong A, Yang GX, Nadler S, et al. Therapeutic effect of cytotoxic T lymphocyte antigen 4/immunoglobulin on a murine model of primary biliary cirrhosis. Hepatology 2013;57(2): 708–715 Genovese MC, Becker JC, Schiff M, et al. Abatacept for rheumatoid arthritis refractory to tumor necrosis factor alpha inhibition. N Engl J Med 2005;353(11):1114–1123 Kremer JM, Dougados M, Emery P, et al. Treatment of rheumatoid arthritis with the selective costimulation modulator abatacept: twelve-month results of a phase iib, double-blind, randomized, placebo-controlled trial. Arthritis Rheum 2005;52(8):2263–2271 Abrams JR, Lebwohl MG, Guzzo CA, et al. CTLA4Ig-mediated blockade of T-cell costimulation in patients with psoriasis vulgaris. J Clin Invest 1999;103(9):1243–1252 Zhernakova A, van Diemen CC, Wijmenga C. Detecting shared pathogenesis from the shared genetics of immune-related diseases. Nat Rev Genet 2009;10(1):43–55 Kita H, Matsumura S, He XS, et al. Quantitative and functional analysis of PDC-E2-specific autoreactive cytotoxic T lymphocytes in primary biliary cirrhosis. J Clin Invest 2002;109(9): 1231–1240 Becher B, Durell BG, Noelle RJ. Experimental autoimmune encephalitis and inflammation in the absence of interleukin-12. J Clin Invest 2002;110(4):493–497

mon denominators in primary biliary cirrhosis: the role of IL-12. J Hepatol 2012;56(3):731–733 Yoshida K, Yang GX, Zhang W, et al. Deletion of interleukin-12p40 suppresses autoimmune cholangitis in dominant negative transforming growth factor beta receptor type II mice. Hepatology 2009;50(5):1494–1500 Mannon PJ, Fuss IJ, Mayer L, et al; Anti-IL-12 Crohn’s Disease Study Group. Anti-interleukin-12 antibody for active Crohn’s disease. N Engl J Med 2005;352(12):1276 Burakoff R, Barish CF, Riff D, et al. A phase 1/2A trial of STA 5326, an oral interleukin-12/23 inhibitor, in patients with active moderate to severe Crohn’s disease. Inflamm Bowel Dis 2006;12(7): 558–565 Leonardi CL, Kimball AB, Papp KA, et al; PHOENIX 1 study investigators. Efficacy and safety of ustekinumab, a human interleukin-12/23 monoclonal antibody, in patients with psoriasis: 76-week results from a randomised, double-blind, placebo-controlled trial (PHOENIX 1). Lancet 2008;371(9625): 1665–1674 Hochdörfer T, Kuhny M, Zorn CN, et al. Activation of the PI3K pathway increases TLR-induced TNF-α and IL-6 but reduces IL-1β production in mast cells. Cell Signal 2011;23(5):866–875 Frey RS, Gao X, Javaid K, Siddiqui SS, Rahman A, Malik AB. Phosphatidylinositol 3-kinase gamma signaling through protein kinase Czeta induces NADPH oxidase-mediated oxidant generation and NF-kappaB activation in endothelial cells. J Biol Chem 2006;281(23):16128–16138 Koyasu S. The role of PI3K in immune cells. Nat Immunol 2003; 4(4):313–319 Varjosalo M, Taipale J. Hedgehog: functions and mechanisms. Genes Dev 2008;22(18):2454–2472 Ingham PW, McMahon AP. Hedgehog signaling in animal development: paradigms and principles. Genes Dev 2001;15(23): 3059–3087 Bhardwaj G, Murdoch B, Wu D, et al. Sonic hedgehog induces the proliferation of primitive human hematopoietic cells via BMP regulation. Nat Immunol 2001;2(2):172–180 Jung Y, McCall SJ, Li YX, Diehl AM. Bile ductules and stromal cells express hedgehog ligands and/or hedgehog target genes in primary biliary cirrhosis. Hepatology 2007;45(5):1091–1096 Omenetti A, Popov Y, Jung Y, et al. The hedgehog pathway regulates remodelling responses to biliary obstruction in rats. Gut 2008;57(9):1275–1282 Omenetti A, Syn WK, Jung Y, et al. Repair-related activation of hedgehog signaling promotes cholangiocyte chemokine production. Hepatology 2009;50(2):518–527 Tacke F, Luedde T, Trautwein C. Inflammatory pathways in liver homeostasis and liver injury. Clin Rev Allergy Immunol 2009; 36(1):4–12 Locksley RM, Killeen N, Lenardo MJ. The TNF and TNF receptor superfamilies: integrating mammalian biology. Cell 2001;104(4): 487–501 Del Villar K, Miller CA. Down-regulation of DENN/MADD, a TNF receptor binding protein, correlates with neuronal cell death in Alzheimer’s disease brain and hippocampal neurons. Proc Natl Acad Sci U S A 2004;101(12):4210–4215 Sleiman PM, Flory J, Imielinski M, et al. Variants of DENND1B associated with asthma in children. N Engl J Med 2012;366(7): 672 Kitamura K, Nakamoto Y, Akiyama M, et al. Pathogenic roles of tumor necrosis factor receptor p55-mediated signals in dimethylnitrosamine-induced murine liver fibrosis. Lab Invest 2002; 82(5):571–583 Lleo A, Bowlus CL, Yang GX, et al. Biliary apotopes and antimitochondrial antibodies activate innate immune responses in primary biliary cirrhosis. Hepatology 2010;52(3):987–998

36

37

38 39

40

41

42

43

44

45

46 47 48 49

50

51

52

53

54

55

Seminars in Liver Disease

Vol. 34

No. 3/2014

57

58

59

60

61

62

63 64 65

66

67

68

69

70

71

72

73

74

75

This document was downloaded for personal use only. Unauthorized distribution is strictly prohibited.

262

Genetics and Epigenetics of Primary Biliary Cirrhosis

77

78 79

80

81

82

83

84

85

86

87 88

89

90

91

92 93

94

95

96

alpha and transforming growth factor-beta reflect severity of liver damage in primary biliary cirrhosis. J Gastroenterol Hepatol 2002;17(2):196–202 Pessach IM, Notarangelo LD. X-linked primary immunodeficiencies as a bridge to better understanding X-chromosome related autoimmunity. J Autoimmun 2009;33(1):17–24 Lleo A, Moroni L, Caliari L, Invernizzi P. Autoimmunity and Turner’s syndrome. Autoimmun Rev 2012;11(6-7):A538–A543 Selmi C, Invernizzi P, Zuin M, Podda M, Seldin MF, Gershwin ME. Genes and (auto)immunity in primary biliary cirrhosis. Genes Immun 2005;6(7):543–556 Selmi C, Invernizzi P, Miozzo M, Podda M, Gershwin ME. Primary biliary cirrhosis: does X mark the spot? Autoimmun Rev 2004; 3(7-8):493–499 Bogdanos DP, Smyk DS, Rigopoulou EI, et al. Twin studies in autoimmune disease: genetics, gender and environment. J Autoimmun 2012;38(2-3):J156–J169 Invernizzi P, Alessio MG, Smyk DS, et al. Autoimmune hepatitis type 2 associated with an unexpected and transient presence of primary biliary cirrhosis-specific antimitochondrial antibodies: a case study and review of the literature. BMC Gastroenterol 2012; 12:92 Smyk DS, Rigopoulou EI, Lleo A, et al. Immunopathogenesis of primary biliary cirrhosis: an old wives’ tale. Immun Ageing 2011; 8(1):12 Smyk DS, Rigopoulou EI, Pares A, et al. Sex differences associated with primary biliary cirrhosis. Clin Dev Immunol 2012; 2012:610504 Smyk DS, Rigopoulou EI, Pares A, Mytilinaiou MG, Invernizzi P, Bogdanos DP. Familial primary biliary cirrhosis: like mother, like daughter? Acta Gastroenterol Belg 2012;75(2):203–209 Svyryd Y, Hernández-Molina G, Vargas F, Sánchez-Guerrero J, Segovia DA, Mutchinick OM. X chromosome monosomy in primary and overlapping autoimmune diseases. Autoimmun Rev 2012;11(5):301–304 Lleo A, Battezzati PM, Selmi C, Gershwin ME, Podda M. Is autoimmunity a matter of sex? Autoimmun Rev 2008;7(8):626–630 Miozzo M, Selmi C, Gentilin B, et al. Preferential X chromosome loss but random inactivation characterize primary biliary cirrhosis. Hepatology 2007;46(2):456–462 Persani L, Bonomi M, Lleo A, et al. Increased loss of the Y chromosome in peripheral blood cells in male patients with autoimmune thyroiditis. J Autoimmun 2012;38(2-3):J193–J196 Quintana-Murci L, Krausz C, McElreavey K. The human Y chromosome: function, evolution and disease. Forensic Sci Int 2001; 118(2-3):169–181 Chueh FY, Leong KF, Cronk RJ, Venkitachalam S, Pabich S, Yu CL. Nuclear localization of pyruvate dehydrogenase complex-E2 (PDC-E2), a mitochondrial enzyme, and its role in signal transducer and activator of transcription 5 (STAT5)-dependent gene transcription. Cell Signal 2011;23(7):1170–1178 Noelle RJ, Nowak EC. Cellular sources and immune functions of interleukin-9. Nat Rev Immunol 2010;10(10):683–687 Merino R, Fossati L, Lacour M, Izui S. Selective autoantibody production by Yaaþ B cells in autoimmune Yaa(þ)-Yaa- bone marrow chimeric mice. J Exp Med 1991;174(5):1023–1029 Subramanian S, Tus K, Li QZ, et al. A Tlr7 translocation accelerates systemic autoimmunity in murine lupus. Proc Natl Acad Sci U S A 2006;103(26):9970–9975 Fairhurst AM, Hwang SH, Wang A, et al. Yaa autoimmune phenotypes are conferred by overexpression of TLR7. Eur J Immunol 2008;38(7):1971–1978 Santiago-Raber ML, Kikuchi S, Borel P, et al. Evidence for genes in addition to Tlr7 in the Yaa translocation linked with acceleration of systemic lupus erythematosus. J Immunol 2008;181(2): 1556–1562

263

97 Esteller M. Non-coding RNAs in human disease. Nat Rev Genet

2011;12(12):861–874 98 Katoh H, Zheng P, Liu Y. FOXP3: genetic and epigenetic implica-

tions for autoimmunity. J Autoimmun 2013;41:72–78 99 Lu Q. The critical importance of epigenetics in autoimmunity. J

Autoimmun 2013;41:1–5 100 Wang Q, Selmi C, Zhou X, et al. Epigenetic considerations and the

101

102 103 104

105

106

107

108

109

110

111

112 113

114

115

116

117

clinical reevaluation of the overlap syndrome between primary biliary cirrhosis and autoimmune hepatitis. J Autoimmun 2013; 41:140–145 Selmi C, Mayo MJ, Bach N, et al. Primary biliary cirrhosis in monozygotic and dizygotic twins: genetics, epigenetics, and environment. Gastroenterology 2004;127(2):485–492 Gay S, Wilson AG. The emerging role of epigenetics in rheumatic diseases. Rheumatology (Oxford) 2014;53(3):406–414 Pillai S. Rethinking mechanisms of autoimmune pathogenesis. J Autoimmun 2013;45:97–103 Costenbader KH, Gay S, Alarcón-Riquelme ME, Iaccarino L, Doria A. Genes, epigenetic regulation and environmental factors: which is the most relevant in developing autoimmune diseases? Autoimmun Rev 2012;11(8):604–609 Selmi C, Cavaciocchi F, Lleo A, et al. Genome-wide analysis of DNA methylation, copy number variation, and gene expression in monozygotic twins discordant for primary biliary cirrhosis. Front Immunol 2014;5:128 Carrel L, Willard HF. X-inactivation profile reveals extensive variability in X-linked gene expression in females. Nature 2005;434(7031):400–404 Ozbalkan Z, Bagişlar S, Kiraz S, et al. Skewed X chromosome inactivation in blood cells of women with scleroderma. Arthritis Rheum 2005;52(5):1564–1570 Brix TH, Knudsen GP, Kristiansen M, Kyvik KO, Orstavik KH, Hegedüs L. High frequency of skewed X-chromosome inactivation in females with autoimmune thyroid disease: a possible explanation for the female predisposition to thyroid autoimmunity. J Clin Endocrinol Metab 2005;90(11): 5949–5953 Uz E, Loubiere LS, Gadi VK, et al. Skewed X-chromosome inactivation in scleroderma. Clin Rev Allergy Immunol 2008;34(03): 352–355 Ozcelik T. X chromosome inactivation and female predisposition to autoimmunity. Clin Rev Allergy Immunol 2008;34(03): 348–351 Higuchi M, Horiuchi T, Kojima T, et al. Analysis of CD40 ligand gene mutations in patients with primary biliary cirrhosis. Scand J Clin Lab Invest 1998;58(5):429–432 Zheng Y, Rudensky AY. Foxp3 in control of the regulatory T cell lineage. Nat Immunol 2007;8(5):457–462 Padgett KA, Lan RY, Leung PC, et al. Primary biliary cirrhosis is associated with altered hepatic microRNA expression. J Autoimmun 2009;32(3-4):246–253 Qin B, Huang F, Liang Y, Yang Z, Zhong R. Analysis of altered microRNA expression profiles in peripheral blood mononuclear cells from patients with primary biliary cirrhosis. J Gastroenterol Hepatol 2013;28(3):543–550 Banales JM, Sáez E, Uriz M, et al. Up-regulation of microRNA 506 leads to decreased Cl-/HCO3- anion exchanger 2 expression in biliary epithelium of patients with primary biliary cirrhosis. Hepatology 2012;56(2):687–697 Ando Y, Yang GX, Kenny TP, et al. Overexpression of microRNA-21 is associated with elevated pro-inflammatory cytokines in dominant-negative TGF-β receptor type II mouse. J Autoimmun 2013; 41:111–119 Ninomiya M, Kondo Y, Funayama R, et al. Distinct microRNAs expression profile in primary biliary cirrhosis and evaluation of miR 505-3p and miR197-3p as novel biomarkers. PLoS ONE 2013; 8(6):e66086

Seminars in Liver Disease

Vol. 34

No. 3/2014

This document was downloaded for personal use only. Unauthorized distribution is strictly prohibited.

76 Neuman M, Angulo P, Malkiewicz I, et al. Tumor necrosis factor-

Bianchi et al.

Genetics and Epigenetics of Primary Biliary Cirrhosis

Bianchi et al.

118 Qian C, Chen SX, Ren CL, Zhong RQ, Deng AM, Qin Q. [Abnormal

122 Feldmann M, Maini RN. Lasker Clinical Medical Research

expression of miR-let-7b in primary biliary cirrhosis and its clinical significance]. Zhonghua Gan Zang Bing Za Zhi 2013;21(7):533–536 119 Hirschfield GM, Liu X, Han Y, et al. Variants at IRF5-TNPO3, 17q1221 and MMEL1 are associated with primary biliary cirrhosis. Nat Genet 2010;42(8):655–657 120 Liu JZ, Hov JR, Folseraas T, et al; UK-PSCSC Consortium; International IBD Genetics Consortium; International PSC Study Group. Dense genotyping of immune-related disease regions identifies nine new risk loci for primary sclerosing cholangitis. Nat Genet 2013;45(6):670–675 121 Taş S, Avci O. Rapid clearance of psoriatic skin lesions induced by topical cyclopamine. A preliminary proof of concept study. Dermatology 2004;209(2):126–131

Award. TNF defined as a therapeutic target for rheumatoid arthritis and other autoimmune diseases. Nat Med 2003;9(10): 1245–1250 123 Braun J, Davis J, Dougados M, Sieper J, van der Linden S, van der Heijde D; ASAS Working Group. First update of the international ASAS consensus statement for the use of anti-TNF agents in patients with ankylosing spondylitis. Ann Rheum Dis 2006; 65(3):316–320 124 Gisondi P, Girolomoni G. Biologic therapies in psoriasis: a new therapeutic approach. Autoimmun Rev 2007;6(8):515–519 125 Rutgeerts P, Vermeire S, Van Assche G. Biological therapies for inflammatory bowel diseases. Gastroenterology 2009;136(4): 1182–1197

This document was downloaded for personal use only. Unauthorized distribution is strictly prohibited.

264

Seminars in Liver Disease

Vol. 34

No. 3/2014

Copyright of Seminars in Liver Disease is the property of Thieme Medical Publishing Inc. and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use.