Introduction to Primary Immunodeficiencies

Mauno Vihinen

Institute of Medical Technology, University of Tampere, POB 607, FIN-33101, Tampere, Finland

CONTENTS

Primary immunodeficiency diseases (PIDs) are intrinsic defects of the immune system. Patients with PID have increased susceptibility to recurrent and persistent infections, but other symptoms are also common.

Adaptive immune mechanisms recognize and neutralize foreign molecules or microorganisms in a specific manner. Lymphocytes, B and T cells, can respond selectively to thousands of non-self materials. Adaptation is further acquired with memory of previous infections. Immunodeficiencies impair the functioning of the immune system. Deficiencies are highly variable with regard to symptoms, phenotype, genotype, severity, etc, because many cells and molecules are required for both natural and adaptive immunity. However, increased susceptibility to infections is common to all immunodeficiencies.

More than 70 primary immune deficiencies (PIDs) are known, and can be grouped according to the components of the immune system affected.

1) Antibody deficiency disorders are defects in immunoglobulin-producing B cells.

2) T cell deficiencies affect the function in killing infected cells or helping other immune cells.

3) T cell deficiencies result usually in combined immunodeficiencies (CIDs), where both T cells and antibody production are defective.

Other IDs affect the

4) complement system or

5) phagocytic cells

impairing anti-microbial immunity.

Secondary immunodeficiencies may cause similar infections to PIDs, but secondarily to some other pathological condition such as malnutrition, age, drugs, tumours, or infections including HIV in AIDS.

Most PIDs are relatively rare disorders. The incidence of PIDs varies greatly from about 1:500 births with selective IgA deficiency to only a few known cases for the rarest disorders.

Table of prevalences for immunodeficiencies.

Patients with antibody deficiencies are especially susceptible to encapsulated bacteria, which cause pyogenic infections. T cell immunodeficiencies and severe combined immunodeficiencies (SCIDs) are marked with opportunistic infections caused by common environmental microorganisms. PID patients have recurrent, serious infections starting early after birth. Children are protected for 6-12 months by the maternal IgG. Life threatening symptoms can arise already within the first few days of life in SCID.

Infections are treated with antibiotics. PID patients require prolonged treatment with high doses. Antibody deficiencies are treated with intravenous immunoglobulin substitution therapy. Gammaglobulins are extracted from human blood from donor pools. Leukocytes are produced in stem cells in bone marrow. In SCIDs bone marrow transplantation is the most effective treatment. In certain metabolic disorders (ADA and PNP deficiency) enzyme substitution therapy can be applied.

The immune system consists of a large number of molecules and processes, and immunodeficiencies can therefore be caused by genetic alterations at many loci. A particular PID can be caused by defects in any one of several molecules that are required for certain responses, because a defect in any of the sequential steps can impair the system. The inheritance of the majority of the PIDs is autosomal recessive (AR), although the most studied cases are X-linked.

Recognition of the enormous range of non-self substances is the basis of adaptive immunity and is achieved by mechanisms that produce largely heterogeneous receptors, namely antibodies, T cell receptors (TCRs), and the components of the major histocompatibility complexes (MHCs). These molecules owe their high variability to a large number of genetic segments, which can be joined in random fashion.

B cell immunodeficiencies are antibody deficiency disorders that are restricted to antibody function. Either B lymphocyte development is impaired, or B cells fail to respond to T cell signals. All or only selected subsets of immunoglobulins may be deficient. Patients have recurrent pyogenic infections with encapsulated bacteria. Infections require early and vigorous treatment with antibiotics and life-long immunoglobulin replacement therapy.

XLA is a typical antibody deficiency in which production of antibodies is prevented due to a block in the B cell maturation. The prevalence is about 1:200,000. Serum concentrations of IgG, IgA, and IgM are markedly reduced. Levels of circulating B lymphocytes are significantly decreased and plasma cell are absent from lymph nodes and bone marrow, but the number of T cells is normal or even increased. The clinical phenotype may be variable and even members of the same family can have different symptoms. Patients with XLA have normal response to viral infections and normal V(D)J rearrangement. XLA is caused by a block in the B cell differentiation. Btk, the affected protein, is a tyrosine kinase that regulates activity of signalling pathways by phosphorylation.

Typically, about one third of X-linked PIDs are new, sporadic cases, where the mutation has appeared in the patient. Bruton tyrosine kinase (Btk) is the defective molecule in X-linked agammaglobulinaemia (XLA). Mutations in the gene for BTK prevent B cell maturation since Btk is crucial signalling molecule regulating B cell development into antibody-producing plasma cells. Btk protein consists of five domains, all of which can be affected by disease-causing alterations. The majority of the known mutations (altogether more than 300) lead to truncation of the protein due to either nonsense or frameshift mutations because of insertions, deletions or splice site defects. Although the mutations are evenly distributed in the BTK gene, the most mutable single sites in many genetic disorders, including XLA, are CpG dinucleotides.

In addition to the catalytic tyrosine kinase domain, Btk contains modules for protein-protein interactions, namely Tec homology (TH), Src homology 2 (SH2), and SH3 domains. Pleckstrin homology (PH) domain is responsible for membrane localisation of the protein by binding to the phosphatidyl inositol groups of membrane lipids. Btk has several signalling partners. The specificity of the kinase domain may be increased by simultaneous binding of the SH2 and/or SH3 domain into their recognition sites in the substrate. The TH domain binds Zn²⁺, which is essential for stability. Btk is activated by stepwise phosphorylation, first by Src family kinases and then by autophosphorylation.

Although many of the mutations cause truncation of the Btk protein, there are also other types of alterations. For example, a number of structural mutations lead into misfolded proteins. Three-dimensional structures of the Btk domains have been used to describe the consequences of the disease-causing mutations. Of the amino acid-changing missense mutations, many alter structurally of functionally significant conserved residues.

HIM syndrome represents a group of related diseases, the majority of which are X-linked. XHIM is caused by a genetic defect in the gene for the CD40 ligand. The patients have severely reduced IgG, IgA, and IgE serum levels, but normal or even raised IgM levels. In XHIM there is a failure in heavy chain class switch from IgM to IgG and IgA. Interaction between CD40L in T cells and CD40 on B cells is a key signal for the generation of memory B cells and for the formation of germinal centres. Defective CD40L prevents production of certain antibodies. CD40 is also involved in interaction with macrophages and dendritic cells, which induces IL-12 secretion and thereby elicits an immune response to intracellular microorganisms. Infections in patients with HIM are similar to those in XLA, except for higher tendency for persistent or recurrent neutropenia and thrombocytopenia.

CD40 belongs to the tumour necroris factor (TNF) superfamily of transmembrane proteins. Signalling through CD40 activates phospholipase Cγ 2 and phosphatidylinositol-3 kinase, upregulates CD23, CD54, and CD80, and induces transcription factors such as nuclear factor-κ B. The XHIM causing mutations can appear in any of the domains of CD40L (intracytoplasmic, transmembrane, extracellular unique, and TNF homology regions). However, mutations cluster into the TNHF domain. The most common alterations are point mutations, which typically result in truncation of the polypeptide chain.

IgA deficiency can affect only IgA levels, or it may be combined with the lack of other isotypes. IgA deficiency is the most prevalent PID (1:500 Caucasians), but its mechanism remains unknown. Only about one third of the patients are particularly prone to infections. The serum concentrations of the other immunoglobulins are usually normal, but patients have a high incidence of autoantibodies.

IGHG1
IGHG2
IGHG3
IGHG4

Selective deficiencies of IgG subclasses, with or without IgA deficiency, are caused by defects in several genes. IgG2 deficiency is most common in children, whereas adults more often have low levels of IgG3.

Common variable immunodeficiency (CVID) is a group of undifferentiated disorders with defective antibody formation. The incidence is approximately 1:25,000. Patients with CVID usually have normal number of circulating B cells, but low serum levels of IgG and IgA. However, the B cells are defective. CVID affects both females and males equally and it usually has later age of onset than other antigen IDs. Patients have an unusually high incidence of lymphoreticular and gastrointestinal malignancies and the incidence of autoimmune disorders is also increased. CVID forms arise from several different genetic defects.

Other B cell deficiencies have been described including, for example μ heavy chain deficiency; λ 5 surrogate light chain deficiency; and κ light chain deficiency.

T cell deficiencies usually affect also other components of the immune system and lead into CIDs.. Patients have a progressive decrease in the number of circulating T cells, whereas numbers of circulating B cells and serum immunoglobulin are usually normal. Autoimmunity is a frequent complication in T cell IDs. In T cell deficiencies bone marrow transplantation is in many cases the only long-lasting therapeutic option.

Purine nucleoside phosphorylase (PNP) deficiency is characterized by accumulation of toxic purine metabolites, primarily dGTP, in cells. PNP catalyses the phosphorolysis of the purine nucleosides, (deoxy)inosine and (deoxy)guanosine, to purine bases and ribose-1-phosphate. dGTP is particularly toxic to T cells by inhibition of ribonucleotide reductase and further DNA synthesis and proliferation. PNP deficiency is often accompanied by neurologic disorder. The enzyme following PNP in the purine catabolism is adenosine deaminase, mutations of which cause SCID.

T cell activation triggers cascades of reactions. Zap-70 (ζ -associated polypeptide of 70 kDa) is a tyrosine kinase that binds with its SH2 domains to the TCR's phosphorylated immunoreceptor tyrosine-based activation motif (ITAM) sequences. In Zap-70 deficiency, signalling through TCR is defective, influencing T cell development.

In X-linked lymphoproliferative disease (XLP) or Duncan's disease, patients are exceptionally susceptible for Eppstein-Barr virus (EBV). EBV infection causes mononucleosis by vigorous uncontrolled expansion of both T and B cells. The disease is associated usually either with hypogammaglobluninaemia, Burkitt lymphoma, carcinoma, some forms of Hodgkin disease, or several of them. The mortality is complete by the age of 40 years. SAP (SLAM-associated protein) (also called for DSHP and SHD1A) is a short SH2 domain containing molecule. SLAM (signalling lymphocyte activation molecule), also known as CDw150, appears on the surface of T cells, where is has a crucial function in stimulation. Phosphorylation of SLAM provides docking sites for SH2 domain containing proteins including protein phosphatase SHP-2. SAP regulates the binding by competing for the SLAM. Mutations in SAP affect the interaction between T and B cells and leads into uncontrolled B cell proliferation in EBV infection. SAP mutations either truncate the protein or affect the folding or recognition of ligand(s) by its SH2 domain.

Nezelof syndrome is a T cell deficiency with little or no abnormality of gammaglobulins. The patients have very small thymuses. Also antibody synthesis is impaired and IgA can be deficient, whereas IgD or IgE levels can be elevated. Nezelof syndrome is the most likely PID to be confused to AIDS.

CD3E
CD3G

CD3 is a multicomponent T cell complex formed of non-identical subunits that interact with TCR. Interaction with antigen activates cytokine release and cell proliferation. Rare CD deficiencies are caused by mutations in the γ and ε subunits.

In combined B and T cell immunodeficiencies, the most severe IDs, all adaptive immune functions are absent. The condition is fatal unless the immune system can be reconstituted, either by transplants of immunocompetent tissue or by enzyme replacement. The immunological, genetic, and enzymatic characteristics of the diseases show great diversity. SCIDs have an average frequency of approximately 1 in 75,000 births.

In T^-B^- SCID both T and B cells are lacking. To this group of diseases belong RAG1 and RAG2 deficiencies, Omenn syndrome, reticular dysgenesis, and ADA deficiency.

RAG1
RAG2
Omenn syndrome

In recombination activating gene 1 (RAG1) and RAG2 deficiencies and the Omenn syndrome, recombinase-activating proteins are defective. These IDs are autosomal recessive defects. Antibodies as well as T cell receptor and major histocompatibility complexes (MHCs) have very wide spectrum of specificity, which originates from combination of coding genes from a large number of genomic structures. RAGs are crucial proteins in this process by activating V(D)J recombination in the antibodies and T cell receptor genes required for generation of the diversity of the recognition sites. Both RAG proteins are involved in cleaving double stranded DNA during recombination. T cells are very low in the patients, but NK cells may appear in increased numbers.

RAG1 contains homeodomain and a region for RAG2 interaction. RAG2 has been suggested to be formed of a kelch-like propeller structure and a PHD domain. RAG2 mutations appear in both regions. In the Omenn syndrome, recombination is only partially deficient. Some of the Omenn syndrome patients have mutations that lower the efficiency of RAG interactions. RAG1 and -2 disruption blocks the initiation of V(D)J recombination and leads further to complete absence of both mature B and T cells.

Reticular dysgenesis is a very rare autosomal recessive form of SCID, which generally leads to early death. The disease is characterized by lack or very reduced levels of B and T cells, thrombocytes involved in blood clotting, and granulocytes that form the majority of blood leukocytes, due to the failed maturation of not only lymphoid but also of myeloid precursor cells.

Adenosine deaminase (ADA) deficiency accounts for about half of the autosomal recessive forms of SCIDs. ADA follows PNP in purine nucleoside catabolism, but deficiency in this enzyme causes even more severe symptoms than PNP deficiency, which is a T cell deficiency. ADA degrades toxic adenosine and deoxyadenosine, which accumulate in the cells of patients. Immature lymphoid cells are particularly sensitive to these nucleotides. In addition to immunological defect, most patients with ADA deficiency also have skeletal abnormalities.

ADA deficiency is an ideal disease for development of gene therapy methods, because there is selective pressure on nontransduced T cells, because they are not viable. ADA protein is tolerated also when overexpressed. The disorder is treated usually with ADA protein substitution therapy or with bone marrow transplantation.

In T^-B⁺ SCID T cells are missing but B cells can be present even in increased numbers. However, the produced B cells are defective.

X-linked SCID, accounting for about 50-60% of SCID cases, is caused by IL-2 receptor γ chain mutations, which lead to very low numbers of T cells and NK cells, whereas B cells are present in high numbers. However, the B cells are immature and defective. IL-2 receptor (IL-2R) α -chain (CD25) deficiency has also been reported. The γ chain of the receptor forms part of the receptor also for IL-2, -4, -7, -9, and -15, affecting the differentiation and growth of lymphocytes. The γ chain consists of an extracellular domain with WS motif, transmembrane region, as well as intracellular domain with Box1 and Box2 regions. Some 150 different mutations distributed in all the domains have been determined. Patients with X-SCID have extreme susceptibility to infections.

The AR form of SCID is caused by mutations in Janus kinase 3 (JAK3) tyrosine kinase. IL-2 stimulates the receptor and induces tyrosine phosphorylation and further activation of JAK3. The γ c-JAK3 pathway transmits the signal to the nucleus via STATs and effects the transcription of genes that respond to cytokines. Binding to IL-2 causes dimerization of the receptors and leads into activation of JAK3 tyrosine kinase. Activated JAK family members phosphorylate multiple tyrosine residues in the receptors. Signal transducers and activators of transcription (STATs) are transcription factors, which bind with their SH2 domains to the phosphotyrosines in the receptor. Activated, dimerized STATs then dissociate from the receptor and translocate to nucleus, where they bind to enhancer regions in DNA and thereby effect transcription of cytokine-responsive genes. Many defective genes can cause similar symptoms. Mutations in the γ c chain lead to abrogated or defective JAK3-mediated signal transduction.

About 30-40% or T^-B⁺ SCIDs are caused by JAK3 mutations. JAK3 is a tyrosine kinase composed of seven JAK homology (JH) domains. JH1 is the kinase domain and JH2 a kinase-like module. SCID-causing mutations have been found from several domains. This seems to be typical for multidomain signalling proteins since function can be impaired even when the kinase activity is normal if the enzyme cannot bind effectively to its substrate(s) or partner(s). Majority of the mutations lead into truncation or rearrangement of the JAK3 protein from the pseudokinase domain.

Other combined B and T cell deficiencies include MHC class I deficiency, which is due to peptide transporter protein 2 (TAP2) mutations.

TAP2 transports peptides from the cytoplasm into endoplasmic reticulum, where MHC I molecules can bind to them. Cells degrade foreign proteins by proteolysis and generate peptides. Processed peptides bind to MHC I molecules, which are transported to the cell surface. Then, cytotoxic T cells recognize the antigen-presenting MHC proteins and kill the infected cells.

CIITA
RFX1
RFX2
RFX3
RFX5
RFXAP
RFXANK

MHC II is expressed in B cells as surface molecule, which presents processed peptide fragments to the TCR of CD4⁺ T helper cells, triggering the antigen-specific T cell response. MHC class II deficiencies impair transcription of MHC II genes. Three forms have been found. Proteins in these groups are parts of regulatory factor (RF) X, a complex binding to the X-box of MHC II promoters in the nucleus. In complementation group A, class II transcription activator (CIITA) is mutated. CIITA is a positive regulator of MHC class II gene transcription, but it does not bind directly to DNA. Regulatory factor RFX 5 is mutated in complementation group C deficiency and it has a DNA-binding domain. RFX-associated protein (RFXAP) binding to RFX5 is mutated in the complementation group D. CD4⁺ T cells are decreased in all three forms, although circulating lymphocyte numbers are normal and immunoglobulin numbers can also be decreased.

Wiskott-Aldrich syndrome (WAS) is an immunodeficiency disorder of both T and B cells characterized by thrombocytopenia, eczema, and recurrent infections. Patients have progressive lymphopenia. WAS is an X-linked immunodeficiency. Female carriers are phenotypically normal since the defective X chromosome is preferentially inactivated. Boys with WAS have increased serum IgA and IgE levels, whereas IgM is decreased. T cells are defective and they have fewer microvilli on the cell surface than normal cells. WAS patients with autoimmune manifestations are at a high risk of getting malignancies. WAS leads to death within first two decades of life because of viral or bacterial infections without bone marrow transplantation.

The gene for WAS has been identified. WAS protein (WASP) interacts with Cdc42, a GTP-binding protein, that has function in cytoskeleton reorganization. Defective cell polarization due to WASP mutations could affect also B cell T cell interactions. WASP consists of several domains, from the N-terminus partly overlapping pleckstrin homology (PH) and WASP homology 1 (WH1) domains, GTPase binding domain, proline rich region and WH2 domain. The proline rich region interacts with adaptor protein Nck. More than 100 WAS-causing mutations scattered along the gene and protein are known. WASP mutations are mainly amino acid substitutions or nonsense mutations leading to truncation of the protein.

DiGeorge syndrome is a congenital immune disorder characterized by lack of embryonic development or underdevelopment. Thymic epithelium is derived from the third and fourth pharyngeal pouches by the sixth week of gestation. The syndrome is associated with several defects and it has been called also for CATCH22, because the gene defect is usually a deletion in chromosome 22, and the symptoms include Cardiac abnormalities, Abnormal facies, Thymic hypoplasia, Cleft palate, and Hypocalcinaemia. The degree of thymus problems varies and only about 20% of the patients have the function or levels of T cells decreased.

Ataxia telangiectasia (AT) is a rare, AR, progressive, neurodegenerative childhood disease that affects the nervous and other body systems. The prevalence of AT is in the order of 1:40,000 to 1:100:000 births. The first signs of the disease usually occur during the first decade of life. AT means ataxia, lack of muscle control, and telangiectasias (tiny, red "spider" veins) first in the corners of the eyes or on ears and cheeks. Immune system is impaired in many patients and they are also predisposed to leukemia and lymphoma and they are extremely sensitive to radiation exposure. About 70% of the patients have IgA deficiency and also some IgG subclasses can be reduced. At the moment there is no cure for AT.

The defective protein, ATM, is a protein kinase that reacts to DNA damage and affects the accumulation of a tumor suppressor p53, which is defective in many cancers. ATM mutations delay the accumulation of p53, allowing cells to replicate without repair of the damaged DNA and thereby increasing the risk of cancer. Large number of AT-causing mutations have been identified from different parts of the molecule.

Combined immunodeficiencies can arise also in association with other diseases or secondarily to other disorders. A great number of disorders are related to immunological deficiencies, although the main defect affects some other functions.

Chromosomal defects as Down syndrome, also known as trisomy 21, Turner syndrome and rings or deletions of chromosome 18 lead into immunodeficiencies. In Down syndrome, serum IgM is progressively reduced and thymus can be defective. The patients have facial abnormalities, but also mental retardation. The triplicated chromosome region contains gene for interferon receptor and therefore the patients suffering of Down syndrome are more sensitive to interferons than normal population.

Abnormalities in chromosome 18 may lead to decreased serum IgA levels and also antibody formation can be impaired.

Turner syndrome patients have generally normal numbers of T and B cells, but serum IgG and IgM levels are reduced.

Chromosomal instability can cause immunodeficiency among other disorders.

Another cause of immunological symptoms is defective repair of errors in DNA.

FANCA
FANCB
FANCC
FANCD
FANCE
FANCF
FANCG
FANCH

Fanconi anaemia is an AR defect of several organs including bone marrow. T cell functions and serum IgA levels are decreased.

Bloom syndrome is marked by chromosomal breakage disorder affecting multiple systems and characterized primarily by telangiectatic erythema and short stature. The patients have reduced T cell levels sometimes accompanied by reduced antibody levels.

XPA
XPB
XPC
XPD
XPE
XPF
XPG
XPI

Xeroderma pigmentosum and DNA ligase 1 defects are photosensitive dermatoses. Sunlight causes skin lesions for patients with these diseases.

ICF syndrome has got its name from immunodeficiency, centromeric instability, facial abnormalities. Serum IgG, IgM, and IgA levels are usually decreased.

In Nijmegen breakage syndrome microcephaly, short stature and recurrent infections are typical. Both B and T cell functions are impaired.

Several metabolic defects are accompanied by immunodeficiencies. These disorders include for example glycogen storage disease type 1b, mannosidosis, methylmalonic acidaemia, acrodermatitis enteropathica, type 1 hereditary orotic aciduria, and transcobalamin 2 deficiency. The degree of immunological problems varies between and within the diseases.

Hypercatabolism of immunoglobulins can also be cause to immunodeficiencies for example in familial hypercatabolism or intestinal lymphangiectasis.

Skeletal abnormalities in cartilage-hair hypoplasia and short-limbed skeletal dysplasia can cause also immunological symptoms.

A number of dermatological defects affect also T and B cell responses. These disorders include Netherton syndrome, dyskeratosis congenita, and Papillon-Lefèvre syndrome among others.

Generalized growth retardation is often associated with infections. A number of these conditions affect the adaptive immunity.

Chronic mucocutaneous candidiasis patients have persistent cadidial infections on mucosa and skin. They have severely impaired immunity to Candida.

Hyper-IgE syndrome, Job syndrome, is a disorder of neutrophil oxidative metabolism, typically with extremely high serum IgE levels, chronic eczema, and recurrent skin and sinopulmonary tract infections

Adaptive immunity: acquired specific immunity.

Autosomal recessive: both genes at a locus are required to confer a trait in other than X or Y chromosome.

B cell: antibody producing blood cell.

Bone marrow transplantation: blood cells are produced in bone marrow, in the central cavities of bones. To reconstitute the missing production of blood cells bone marrow can be transplanted to immunodeficiency patients.

Complement: protein system that recognizes and kills microorganisms.

Gene therapy: substitution of a defective gene in patients with a functional one.

Natural immunity: inborn, non-specific immunity.

T cell: lymphocyte that either helps or activates other cells (T helper) or kills infected cells (cytotoxic T cell).

X-linked: inherited by boys from the mothers in X-chromosome.