Autoimmune Liver Disease

Management and Clinical

Practice
Concepts of Autoimmunity Relevant to Autoimmune Liver Diseases
Isaiah G. Roepe1 and John M. Vierling2
ACHMAD FIKRY
Introduction
• The genesis of autoimmunity requires loss of immune tol­erance to
self‐antigens and results from the complex interplay of genetic,
epigenetic, immunologic, and environmental factors.
• Genetics confers susceptibility for autoimmunity, not for a specific
autoim­mune disease. Thus, susceptible patients often have more than
one autoimmune disease
• “bad genes, bad luck”
• Autoimmune hepatitis (AIH), primary bil­iary cholangitis (PBC), and
primary sclerosing cholangitis (PSC) are classified as autoimmune liver
diseases (AILDs).
Introduction
Thus, this chapter addresses five major themes:
1) innate and adaptive immu­nity in the context of the liver as an
immune organ;
2) generation and maintenance of tol­erance to autoantigens;
3) risk factors for autoimmunity;
4) loss of immune tolerance to autoantigens and perpetuation of
autoimmune diseases; and
5) prospects for prevention of autoimmunity and therapeutic control
of autoimmune diseases.
1) Role of Innate and Adaptive Immunity in Autoimmunity
in the Context of the Liver as an Immune Organ
Innate Immunity Liver as an
Innate Immune Organ
• The innate immune system responds imme­ diately to PAMPs,
comprising microbial con­ stituents, and to DAMPs, comprising cellular
constituents from stressed, neoplastic or dying cells
• The liver is an essential innate immune organ that must either tolerate or respond to
microbial PAMPs, toxins, xenobiotics, food antigens, microbial pathogens, and neo­
plastic cells .
• The liver contains special­ ized liver sinusoidal endothelial cells (LSECs) and large
quantities of Kupffer cells, DCs and NK, NKT and γδT cells.
• The liver also synthesizes C′ proteins, acute‐phase reactant proteins, and multiple
cytokines. PAMP and DAMP activation of TLRs on Kupffer cells, LSECs, hepatocytes, DCs
and HSCs primarily generates IL‐10, providing an immunosuppressive environ­ment.
• The reticuloendothelial function of the liver normally prevents PAMPs, DAMPs and
microbial antigens in portal venous blood from entering the systemic circulation.
Adaptive Immunity and Adaptive
Immune Functions of the Liver
• the adaptive immune system in autoimmunity generates multiple,
delayed, autoantigen‐specific effector immune responses, most occur
in lymph nodes and spleen; thus, effector cells must circulate to
tissues expressing autoantigens to mediate immuno­pathology.
• Polymorphic class III HLA alleles encode immune response proteins,
including TNF‐α/β, complement (C′) factors and heat‐shock proteins.
The balance bet­ ween proinflammatory and anti‐inflammatory
cytokines produced by local innate immune responses determines the
polarization of cytotoxic mechanisms of the adaptive immune
response
Role of the Liver as an Adaptive Immune Organ
• The normal liver is a distinct “lymphoid” compartment containing CD8 αβ T cells, activated CD4 and CD8 T
cells, γδT cells, memory T cells and B cells.
• hepatic DCs, LSECs, and HSCs also function as APCs for intrahepatic T‐cell activation of adaptive immunity.
• Hepatocytes and cholangiocytes may also serve as APCs after cytokine stimulation. CD4 T cells activated by
hepatic APCs pri­marily differentiate into Th2 cells, secreting immunosuppressive IL‐10 and IL‐4.
• Frequently, CD8 T cells activated in the liver have functional deficiencies leading to pre­ mature apoptosis.
However, LSECs can directly activate functional antigen‐specific CD8 CTLs in the liver by cross‐presentation of
soluble exogenous antigens in class I HLA molecules.
• Hepatic Kupffer cells regulate T‐cell homeostasis by inducing apoptosis of senes­ cent T cells expressing CD95
(Fas), TNF‐ apoptosis‐inducing ligand (TRAIL), and programmed cell death 1 (PD‐1) receptors.
• Mucosal invariant T (MAIT) cells have characteristics of both innate and adaptive immune cells that are
relevant in AILDs. MAIT cells have invariant TCR α‐chains that respond to bacterially processed vitamin B
antigens presented by unique major histocompatibility complex (MHC) class I‐ related molecules (MR‐1) on
APCs.
• Normally found only in blood, gut mucosa and mesen­ teric lymph nodes, MAIT cells congregate in the portal
tracts of patients with chronic liver diseases, including AIH, PBC, PSC, alcoholic and non‐alcoholic fatty liver
diseases, and chronic hepatitis C virus (HCV) infection.
2. Generation and Maintenance
of Tolerance to Self‐antigens
Overview
• Immune tolerance is the ability of the immune system to identify and
respond to foreign or non‐self‐antigens, while aborting or controlling
potentially deleterious responses to autoantigens.
• Broadly, immune tolerance is divided into two cate­gories: natural and
inducible tolerance. In addition, natural tolerance has been subclas­
sified as either central or peripheral, based the anatomic site of
development.
Central Tolerance
• Central tolerance involves clonal deletion, clonal anergy or receptor
editing to eliminate autoreactive αβT cells in the thymus and
autoreactive B cells in the bone marrow.
Central T‐cell Tolerance
• T cells with high affinity TCRs for self HLA–self peptide complexes are eliminated in the thymus by clonal deletion.
This process of negative selection favors the survival of T cells with TCRs that exhibit either no or very low affinity for
self‐HLA– autoantigen peptide complexes.
• Overall, more than 95% of T cells generated in the thymus undergo deletion because of excessive self‐reactivity,
which underscores the high frequency of autoreac­tive TCRs among T cells.
• Negative selection of autoreactive T cells by is mediated by the coordinated display of self‐HLA molecules containing
self‐pep­tides generated by expression of genes con­trolled by the autoimmune regulator (AIRE) transcription factor.
• In addition to DCs, medullary thymic epithelial cells (mTECs) selectively express AIRE, which drives tissue‐specific self‐
antigen expression required for deletion of T cells with TCRs that react strongly with autoantigens. In addition, thymic
B class switching also pro­motes central tolerance through negative selection of CD4 T cells.
• AIRE is also involved in peripheral T‐cell tolerance and is expressed in peripheral lymph nodes and the spleen where it
mediates elimination of autoreac­tive extrathymic T cells.
• Thymic editing of TCRs plays a seminal role in the genesis of the TCR repertoire and is mediated by recombination
activating gene (RAG)‐1 and RAG‐2 proteins. After RAG proteins are induced during T‐cell development, they cause
TCR β‐chain rear­rangement and expression of prefabricated TCR α‐chains to form pre‐TCRs.
• A subsequent round of RAG protein induction transcribes rearranged TCR α‐chains that displace prefabricated α‐
chains. Yet another round of induction of RAG proteins finalizes rearrangements of α‐chains, forming functional α/β
TCRs to undergo thymic selec­ tion. This thymic process of TCR editing has a counterpart in the periphery, referred to
as TCR revision, which can generate an unlimited array of antigen‐specific TCRs, overcoming the effects of thymic TCR
selec­tion.
Central B‐cell Tolerance

• B cells develop tolerance to self‐antigens in the bone marrow by both

B‐cell receptor (BCR) editing and clonal deletion of autore­ active B
cells .
• BCR editing results from the induction of VDJ recombinase and rear­
rangements which lead to production of new immunoglobulin‐edited
light chains that modify the specificity of BCRs to prevent recognition
of autoantigens.
Peripheral Tolerance

• Central immunologic tolerance for both T and B cells occurs in the

early developmental stages of both lineages. Additional mecha­ nisms
are required, however, to achieve toler­ ance to self‐antigens that are
not expressed during fetal or neonatal life or are expressed exclusively
in peripheral non‐lymphoid organs .
T‐ and B‐cell Clonal Anergy

• Clonal anergy is a major mechanism in the generation and maintenance of

peripheral tolerance to self‐antigens.
• Autoreactive T‐cell clones not deleted in the thymus or the peripheral
lymphoid tissues may become anergic to autoantigens if TCR activation
occurs in the absence of obliga­tory costimulation.
• Lack of costimulation results in inadequate secretion of IL‐2 and growth
factors required for T‐cell clonal proliferation and maturation of effector
functions. Without costimulation, autoanti­ gen‐specific T cells cease to
differentiate and fail to respond if reexposed to autoantigen.
• Anergic B cells have reduced surface IgM, impaired signal transduction and
short lifes­pans, and exhibit anergy to autoantigen reexposure.
T‐cell Mediated Immune
Regulation
• A subclass of CD4 T cells referred to as Tregs are essential for peripheral tolerance and
maintenance of immune homeostasis (Figure 2.2).
• Tregs mediate immune tolerance by functionally suppressing all activated CD4 T‐cell subsets and
CD8 CTLs. Thus, reductions in the numbers or functional capacity of Tregs can facilitate
autoimmunity and autoimmune diseases. Phenotypically, Tregs are CD4, CD25, fork­ head box P3
(FoxP3) T cells.
• FoxP3 is the key regulator of Treg function, as shown by monogenic deficiency in FOXP3 that
results in immunodysregulation, polyendocrinopa­thy and enteropathy X‐linked (IPEX) syn­drome .
FoxP3‐deficient mice also develop autoimmune diseases, which can be pre­vented by adoptive
transfer of CD4, CD25,
• FoxP3 Tregs. FoxP3 Tregs secrete immuno­ regulatory and immunosuppressive cyto­ kines,
including, IL‐9, IL‐35, IL‐10 and transforming growth factor (TGF)‐β.
• Treg upregulation of intracellular cyclic AMP directly inhibits cell proliferation and reduces
production of IL‐2 required for T‐cell proliferation.
Natural and Inducible T
Regulatory Cells
• Tregs are classified as natural Tregs (nTregs) or inducible Tregs (iTregs). nTregs are produced in
the thymus and represent 5–10% of the total CD4 T‐cell population.
• Despite having a relatively high affinity for autoantigens, nTregs escape clonal deletion in the
thymus. In the periphery, nTregs act as autoantigen‐specific sentinels within the lymph nodes
and spleen to maintain peripheral tolerance.
• They do so by inhibit­ing autoantigen activation of T cells by APCs, causing direct cytotoxicity
of auto­antigen‐activated T cells and secreting anti‐inflammatory cytokines IL‐10 and TGF‐β.
• iTregs are a subset of CD4 T cells activated in the periphery (Figure 2.2). When naive CD4 T
cells (CD4 Th0 cells) are activated in the presence of IL‐10, IL‐4 and TGF‐β, they differentiate
into antigen‐specific CD4, CD25, FoxP3 iTregs.
• Both foreign antigens and autoantigens can generate antigen‐ specific iTregs, conferring
immunoregula­ tory importance in both normal immunity and autoimmunity. iTregs suppress
effector CD4 T‐cell subsets and cytotoxic CD8 T cells by secreting immunosuppressive IL‐10
and TGF‐β, inducing cell cycle arrest and effector T‐cell apoptosis.
• iTregs block the costimulation and maturation of DCs. Among iTregs (Figure 2.2), the T
regulatory 1 (Tr1) subclass exclusively secretes IL‐10 but does not express FoxP3. In contrast,
the T helper 3 (Th3) subclass exclusively secretes TGF‐β.
Peripheral B‐cell Regulatory
Mechanisms
• Activated B regulatory cells (Bregs) also secrete immunosuppressive cytokines IL‐10,
IL‐35 and TGF‐β. IL‐10 and IL‐35 render CD4 Th1 and Th17 cells incapable of medi­
ating immunopathology or producing proin­ flammatory cytokines [12]. In contrast,
Breg secretion of TGF‐β promotes antigen‐ activated CD4 T‐cell differentiation into
iTregs (Figure 2.2), secreting IL‐10 that inhibits TNF‐α production.
• Additional mechanisms also contribute to B‐cell immu­ noregulation. Secreted IgM
induces anti‐ inflammatory apoptotic bodies to reduce proinflammatory cytokines.
Contact bet­ ween B and CD4 T cells reduces CD4 T‐cell proliferation and secretion of
Th1. Binding of B cell CD95L (Fas ligand) to CD95 (Fas) on T cells induces T‐cell
apoptosis. Secretion of autoantigen‐specific IgG4 inhibits ADCC, C′ activation, and
formation of immune complexes because of the low affinity of IgG4 for Fc receptors,
low capacity to activate C′, and its competition with other antibodies.
Regulatory Dendritic Cells
• DCs are potent professional APCs with the dual roles of initiating
adaptive immune responses against deleterious antigens and maintaining
immunologic homeostasis by inducing antigen‐specific tolerance in the
periphery.
• Only immature DCs exhibit regulatory functions, and immature DCs are
concentrated in the liver. Immunosuppressive cytokines or drugs,
microbial products, interactions with Tregs or NKT cells, and phagocytosis
of apoptotic blebs activate regulatory DCs (DCregs). DCreg presenta­tion
of peptide antigens to CD4 and CD8 T cells contributes to antigen‐specific
toler­ance by inducing T‐cell anergy, inhibiting T‐cell function, promoting
generation of iTregs, and enhancing T‐cell apoptosis.
Immunoregulatory Interplay
Between
Treg and Th17 Cells
•
The interplay and balance between iTregs and pathogenic Th17 cells is pivotal for immuno­regulation. Low concentrations
of IL‐2 promote iTreg proliferation and survival but are suboptimal for Th17 proliferation and differentiation. However, the
adverse effects of low concentrations of IL‐2 on Th17 cells can be overcome by proinflammatory IL‐1β.
• Conversely, high concentrations of IL‐2 drive proliferation of CD4 and CD8 effector cells,
includingTh17cells.iTregsalsoexhibitplas­ ticity based on the cytokine milieu. TGF‐β promotes differentiation of either
iTregs or Th17cellsbyinducingexpressionofFOXP3 and receptor‐related orphan receptor (ROR)γ, respectively.
• The cytokine environ­ment dictates differentiation toward either regulatory iTreg or the proinflammatory Th17
phenotypes. In the absence of IL‐6 and IL‐21 (Figure 2.2), FoxP3 binds to RORγ sup­pressing its transcriptional activity and
pre­ venting Th17 differentiation. In the presence of IL‐6 and IL‐21, FoxP3 dissociates from RORγ, allowing Th17
differentiation. Retinoic acid from gut DCs also suppresses Th17 cells, while expanding iTregs. The resulting balance
between iTregs and Th17 dictates tissue immunopathology in autoim­mune diseases.
• In addition, iTregs and Th17 cells can undergo interconversion. Thus, Th17 cells can convert to immunosuppressive IL‐10‐
secreting cells, and FoxP3‐positive iTregs can convert to Th17 cells. Conversion of iTregs to Th17 cells requires a milieu con­
taining IL‐1β, IL‐6, IL‐23, and TGF‐β. Activated epithelial target cells, including cholangiocytes, secrete cytokines favoring
conversion of iTregs to Th17. Thus, target tis­ sues can produce an imbalance of Th17 and iTregs, intensifying chronic
inflammation.
Risk Factors for Autoimmune
Diseases
Genetics
Complex Genetic and Monogenic Diseases
• Complex genetic diseases require an inter­ play of genes and environmental factors
that may manifest as more than one clinical dis­ease (Figure 2.1) .
• Overall, environmental exposures are more important than genetics in shaping the
immune repertoire. Thus, a person’s “exposome” – the lifelong sum of all
endogenous and exogenous environmental exposures interacting with genetic and
epigenetic factors – can favor autoimmunity or protect against it.
• Genome‐wide association studies (GWAS) in autoimmune diseases, including AILDs,
have demonstrated shared associations with HLA alleles and single nucleotide
polymor­phisms (SNPs) of genes related to innate immunity and adaptive immunity .
HLA Risk Alleles
• The strongest HLA‐associated risks for auto­ immune diseases, including AIH and PSC, but not
PBC, lie within the evolutionarily conserved 8.1 ancestral haplotype: HLA‐A1, Cw7, B8,
TNFAB*a2b3, TNFN*S, C2*C, Bf*s, C4A*Q0, C4B*1, DRB1*03:01, DRB3*01:01, DQA1*05:01,
DQB1*02:01.
• The extended 8.1 haplotype is the result of linkage disequi­librium, indicating an evolutionary
advantage to sequestration of these alleles within class I, II and III HLA loci. These alleles are
impor­tant for robust CD4 and CD8 T‐cell activation and generation of TNF‐α/β and C′ factors.
The 8.1 haplotype is associated with AIH and PSC. Most Caucasians with HLA‐B8, DR3 have
the 8.1 haplotype; however, recombinations have produced additional
• HLA‐DRB1*03:01 haplotypes associated with autoimmune diseases. It is notable that even
healthy persons with the 8.1 haplotype exhibit an enhanced immunologic pheno­type with
autoantibodies, circulating immune complexes, activated T cells, and increased apoptosis of
lymphocytes. The HLA‐DRB1 gene is of interest because it is the most polymorphic gene
within the HLA class II region. Thus, it is not surprising that PBC is associated with the DR
allele HLA‐ DR8. Future studies are needed to define how different HLA alleles contribute to a
break in tolerance and development of specific auto­immune diseases.
Non‐HLA Gene Associations
• Interpreting the risks for autoimmune dis­ eases conferred by non‐HLA genes is prob­ lematic because the
odds ratios for risk of autoimmune diseases are far lower than those for HLA alleles . Polymorphisms in
genes encoding CTLA‐4, TNF‐α, Fas (CD95), TNF‐induced protein 3 (TNFAIP3), macrophage migration
inhibitory factor (MIF), and SH2B adapter protein 3 (SH2B3) have been implicated in susceptibility to
autoimmune diseases, including AILDs.
• CTLA‐4 is critical for downregulating effector immune responses and producing T‐cell senescence. TNF‐α
is a potent proinflammatory effector cytokine and therapeutic target in specific autoimmune diseases.
Dysfunction of genetic variants or deficient levels of TNFα‐induced protein 3‐interacting protein 1 (TNIP1)
predispose normal innate cells to produce abnormal inflammatory responses to innocuous TLR ligands.
• TNFAIP3 is a modifying enzyme for ubiquitin, which may influence antigenicity of self‐proteins. CD95 (Fas)
and CD95L (FasL) variants promote survival of autore­ active T and B cells and modify apoptosis of target
cells. MIF is a proinflammatory cyto­kine in both innate and adaptive immunity. SH2B3 suppresses
cytokine‐induced inflam­mation by downregulating Janus kinases (JAKs)andreceptortyrosinekinases(RTKs).
Several autoimmune diseases also are linked to SNPs in cytokine and cytokine receptor genes. A pertinent
example is the IL23R gene, which encodes a protein that forms a dimer with IL‐12Rβ1 to create the IL‐23
receptor complex required for IL‐23 induction of proinflammatory Th17 cells.
Critical Role of Epigenetics
Transcription Factor Enhancers and Super Enhancers
• Gene transcription is an essential process in autoimmunity and autoimmune disease specificity. Emerging
evidence indicates that the generation and perpetuation of autoim­munity is primarily driven by epigenetics
[16]. Over 90% of the thousands of disease‐ associated SNPs detected by GWAS are localized within non‐
coding regions of DNA, that produce regulatory enhancers, some­times occurring in clusters spanning 50 kb
of DNA, called super enhancers (SEs).
• Multiple enhancers and SEs control the expression of protein‐coding genes. These enhancers, especially SEs,
are especially important drivers of cell‐ and tissue‐specific genes. Enhancer functions are mediated through
transcription‐factor (TF) binding motifs that require TF recruitment and nucleation of transcriptional
machinery. Thus, enhancer activity depends on the local structure of chromatin responsible for the
packaging of DNA in association with histone proteins. Since tightly packed DNA is inaccessible to DNA‐
binding TFs, additional epigenetic mechanisms are required to render DNA accessible to enhancer TFs.
• These processes include methylation of DNA and posttran­ scriptional modification of histones through
methylation, acetylation, or ubiquitination. Epigenetic proteins also interact directly with transcriptional
mechanisms and enhancer DNA can also generate enhancer RNA (eRNA) to increase the amount of
enhancer proteins. Epigenetic long non‐cod­ing RNAs (lncRNAs) are expressed within innate immune cells
and CD4 Th1, Th2, Th17, Tregs, CD8 and B cells.
• lncRNAs directly regulate activation and functions of immune cells. lncRNAs promote suscepti­bility to
autoreactivity and perpetuation in autoimmune diseases, including systemic lupus erythematosus (SLE),
rheumatoid arthritis (RA), multiple sclerosis (MS), and psoriasis.
MicroRNAs
• MicroRNAs (miRNAs) function epigeneti­ cally as posttranscriptional
and posttransla­tional regulators of gene expression [17]. miRNAs and
TFs regulate each other’s expression in feedback loops: TFs are nega­
tively regulated by miRNAs, while miRNAs are positively regulated by
TFs. Compelling evidence indicates that miRNAs control the activation
state of innate macrophages and DCs, activation of T cells, apoptotic
elimina­ tion of activated T and B cells, and the critical balance
between iTregs and Th17 cells in sites of inflammation. To date
multiple miRNAs have been implicated in the immunopathogenesis of
autoimmune dis­eases, including AILDs.
Sex and Sex Hormones
• Most autoimmune diseases have a female predilection. However, PSC is a notable exception among AILDs (Table 2.1).
Sex is genetically binary and imprinting of XX female and XY male genomes occurs in all cells from embryogenesis
throughout life.
• Both innate and adaptive immune cells have sex hormone receptors, and sex hormones contribute to the
development and activity of the immune repertoire (Figure 2.1). Yet it is unclear whether female predominance in
autoimmune diseases reflects regulatory mechanisms related to sex‐linked genes, sex‐specific hormones or a
combination of both.
• Females normally produce higher titers of antibodies, more autoantibodies and greater cell‐mediated immunity to
infections and immunization than do normal males. In addition, there is a gender bias in AIRE expression in the
thymus, which may impact deletion of autoreactive clones and formation of nTregs and Bregs. Estrogen levels are
also immu­noregulatory: high levels inhibit CD4 Th1‐ mediated cellular responses and promote CD4 Th2 antibody‐
mediated responses.
• Prolactin, progesterone and testosterone also regulate immune responses by modu­lating expression of estrogen
receptors and altering cytokine secretion. However, the effects of estrogen and other sex hormones in adult women
do not explain the female predilection for autoimmunity in children or elderly adults. Postulated explanations include
skewed X chromosome activation, X monosomy, and microchimerism.
• Beginning during embryogenesis and continuing through life, either the maternal or paternal X chromosome within
each cell is inactivated, forming a Barr body adjacent to the nucleolus. Thus, females are a mosaic of two cell types,
based on the parental source of the active X chromosome. Skewing of X inactivation varies widely and increases with
age. Thus, some X‐linked autoantigens might theoretically escape central or peripheral tolerance.
• The proximity of Barr bodies to the nucleolus suggested that they may interact to expose cryptic autoantigens. X
monosomy might promote autoimmunity by preventing tol­erance to autoantigens encoded by both X chromosomes.
Entry of fetal hematopoietic stem cells into the maternal circulation during pregnancy can cause fetal–maternal micro
chimerism that could promote loss of self‐tolerance.
Vitamin D and Sunlight
Exposure
• In addition to its roles in bone mineralization and calcium homeostasis, vitamin D modu­lates
immune reactions and risk for autoim­ munity Both vitamin D deficiency and genetic
polymorphisms in the vitamin D receptor (VDR) increase the incidence and severity of
multiple autoimmune diseases. Conversely, high vitamin D levels reduce the risk of MS.
Reduction in sunlight exposure and synthesis of 1,25‐dihydroxyvitamin‐D3 (D3) might explain,
in part, the strong correlation between the incidence of autoim­mune disease and increasing
latitude.
• SNPs in two VDR genes, BsmI and TaqI, are associated with AILDs. SNPs in these genes and
FokI are associated specifically with AIH. Dietary vitamin D and vitamin D synthesized in
response to ultraviolet‐B radiation in sunlight determine serum vitamin D levels. Sequential
hydroxylation in the liver and kidney produce D3, the most potent ligand for VDRs. Innate and
adaptive immune cells express VDRs that induce multiple immunologic effects.
• For example, D3 regulates production of antimicrobial peptides and reactive oxygen species in
innate immune cells and promotes NKT cell immunomodulatory functions. D3 also
downregulates immunopathogenic CD4 Th1 and Th17 cells, while upregulating
immunosuppressive CD4 Th2 cells and iTregs. By reducing Th1 secretion of IL‐2, D3 not only
inhibits proliferation of CD4 and CD8 effector T cells but also generates low IL‐2 levels,
favoring proliferation of functional iTregs.
3. Loss of Immune Tolerance to Autoantigens
and Perpetuation of Autoimmune Diseases
Overview
• Autoimmune diseases are uncommon, despite the high frequency of
genetic suscep­tibility and environmental exposure to microbial pathogens
and xenobiotics, including drugs. Autoimmunity requires four essentials.
First, environmental triggers are required to initiate loss of tolerance to
autoantigens in susceptible individuals (Figure 2.1).
• Second, the individual must have HLA alleles that facilitate autoantigen
activation of T cells. Third, T cells must express autoreactive TCRs. Fourth,
the individual must fail to immunoregulate the response to autoantigens.
Evidence that low levels of autoimmune reactions are common in healthy
people highlights the fact that
• these initial steps are common but only dele­terious when not immuno
regulated. GWAS indicates that failure to immunoregulate an autoimmune
reaction is dictated by epige­netic SNPs for enhancers and SEs of gene
expression more than SNPs for HLA and non‐HLA proteins. Moreover, these
SNPs are critical drivers of the cell and tissue spec­ificity of autoimmune
diseases. Multiple factors and mechanisms to break tolerance to self‐antigens
have been identified.
• The increasing incidence of autoimmunity and inflammatory diseases observed
world­ wide is correlated with changes in environ­ mental factors, including a
more modern lifestyle, improved hygiene, a Western diet, use of antibiotics,
and elimination of childhood parasitic infections. Each of these affect the
composition and function of the gut microbiota. Although the proposed causal
link between the gut microbiome and autoimmunity has not been proved,
available data indicate that interplay between the gut microbiota and the
innate and adaptive immune systems of the intestine and liver plays key roles
in both normal and dysfunc­tional systemic immunity.
Role of the Microbiome
• The gut microbiome has been implicated in autoimmunity (Figure 2.1). The gut microbiota change
dynamically under the influence of aging, sex hormones, diet, water purity, hygiene, sanitation,
pollution, exposure to pathogens, use of antibiotics, and the integrity of the gut–blood barrier. Gut
microbiota are composed of commensal bacteria, fungi and viruses, as well as poten­tially
pathogenic bacteria and fungi. In addition, the microbiota process food, xenobiotic pollutants and
drugs to generate micronutrients and metabolites. Intestinal immune responses and the leakiness
of the mucosa dictate the types and concentrations of PAMPs, DAMPs, cytokines, microbes, and
food antigens entering the portal vein for processing in the liver. PAMPs and DAMPs stimulate
enterocyte inflammasomes leading to secretion of proinflammatory cytokines.
• As discussed earlier, bacterial metabolites of vitamin B are the activating antigens for MAIT cells.
Thus, the gut microbiome and intestinal immune responses appear to influence systemic immunity,
and risk for autoimmunity, through the innate and adaptive immune responses of the liver.
• Altered composition of the gut microbiota, referred to as “dysbiosis,” has been reported in
autoimmune diseases, including AILDs. Whether dysbiosis is the cause or the effect of
autoimmunity remains a key unresolved issue. Female sex hormones can also alter the gut
microbiome, which may contribute to the female predilection in autoimmunity. If an altered gut
microbiota or increased gut permeability were causally related to autoim­mune diseases, then
restoration of a normal microbiota and mucosal integrity could be therapeutic.
Mechanisms of Loss of Tolerance to Autoantigens
Bacterial and Viral Infections
• Bacterial, fungal or viral infections can insti­ gate innate and adaptive immune
responses that result in autoimmunity [21]. Migration of neutrophils to sites of
infection or sterile inflammation mediated by IL‐8, IFN‐γ, C3a, C5a, and leukotriene
B4 plays a key role. Neutrophil phagocytosis of microbial organ­ isms and particles
leads to release of soluble antimicrobials and formation of neutrophil extracellular
traps (NETs) comprising chromatin and proteases that enmesh and kill microbes.
The proteolytic function of NETs also can generate neoantigens or microbial
peptide molecular mimics of auto­antigens (see next section).
• Superantigens are proteins produced by pathogenic bacteria and viruses that
trigger non‐antigen‐specific polyclonal T‐cell activation of up to 20% of the host’s T
cells. These activated T cells create a cytokine storm of secreted cytokines,
especially IFN‐γ, which activates macrophages to secrete proinflammatory IL‐1β,
IL‐6 and TNF‐α. This proinflammatory environment could promote adaptive
immune responses to autoantigens in dead or dying cells promote adaptive
immune responses to autoantigens in dead or dying cells.
Molecular Mimicry of Autoantigens
• Molecular mimicry is a key mechanism leading to loss of tolerance to
autoantigens. It is defined as the cross‐reactivity of immune responses to
antigenic epitopes of microbial peptides with autoantigenic epi­ topes of host
peptides. Molecular mimicry has been observed between human autoanti­
gens and peptide antigens of several viral, bacterial and fungal pathogens.
Xenobiotics may also function as molecular mimics for autoantigens.
• For example, some haloge­ nated xenobiotics exhibit immunogenic sim­ ilarity
with the lipoic acid‐binding domain of pyruvate dehydrogenase complex
(PDC)‐E2, the primary autoantigen in PBC. Yet molec­ ular mimicry is an
insufficient explanation for a sustained loss of tolerance, which also requires
failure to control the autoimmune response. Thus, molecular mimicry repre­
sents an environmental trigger capable of progressing to autoimmunity.
Molecular mimicry to adjuvants (substances that enhance immune responses
to an antigen) involves nucleosomes or ribonucleoproteins released after cell
death. These molecules mimic viruses by stimulating an antiviral‐ like, innate
immune response with produc­tion of type 1 interferon.
Neoantigens
• Neoantigens, also called cryptic antigens, can elicit autoimmune responses against autoan­
tigenic epitopes that are not immunogenic until modified by either somatic hypermuta­
tions or binding of haptens. Haptens are small molecules, most often metabolites of drugs
or environmental xenobiotics, that are incapable of eliciting an immune response unless
bound to host carrier proteins. Hapten–carrier protein complexes elicit immune responses
against a single hapten epitope and multiple autoepitopes of the car­ rier protein. For
example, haptens generate autoimmunity against cytochrome P450 (CYP)2D6 in type 2
AIH and autoantibodies
• and a minority of patients with chronic HCV infection, whereas haptens bound to UDP‐
glucuronosyltransferase (UGT) in those infected with HCV or hepatitis D virus, and with
Addison disease, APS‐1 syndrome and some drug‐induced liver injuries result in anti‐UGT
reactions. A subset of NK cells develop antigen‐specific memory to haptens, which may be
important for immune responses after hapten re-exposure. Oral sup­plements of lipoic
acid act as a haptens in the immunogenicity of the lipoic acid‐binding site of PDC‐E2, the
principal autoantigen in PBC. Biochemical modifications of self‐ antigens can also increase
the immunoge­nicity of autoantigens. The best example is citrullination, produced by
posttranslational conversion of arginine to citrulline. Since DNA does not encode the
amino acid citrul­line, citrullinated self‐proteins become auto­antigenic, as in RA.
Failure of Apoptosis to Conceal Autoantigens and Eliminate Autoreactive Cells
• Apoptosis is normally an immunologically silent form of cell death. Phagocytic
removal of the corpse (efferocytosis) of apo­ptotic cells and blebs by APCs normally
induces release of anti‐inflammatory mole­cules, inhibits NF‐κB stimulation of proin­
flammatory cytokines, and promotes secretion of anti‐inflammatory IL‐10 and TGF‐
β. Failure of these normal APC mecha­ nisms is an attractive hypothesis for the
genesis of autoimmunity, because apoptotic blebs contain disproportionately high
concentrations of known autoantigens. However, non‐apoptotic forms of cell death,
such as necrosis or necroptosis, result in APC phagocytosis, processing and
presenta­tion of autoantigenic peptides to autoreactive T and B cells in
immunogenetically suscep­tible persons. This is the proposed explana­ tion for AIH
after documented infections with hepatotrophic or other viruses causing
hepatocyte necrosis. Defective apoptosis might also contribute to the persistence
of autoreactive T and B cells in autoimmune diseases. Genetic defects in Fas
(CD95), Fas‐L (CD95L) and RAS pathways cause lymphoproliferative disorders and
autoimmunity due to inability to eliminate autoreactive effector cells.