Immunological and genetic bases of new primary immunodeficiencies

Safety and efficacy of a novel mini-pool intravenous immunoglobulin therapy in children with primary immunodeficiency

BACKGROUND AND OBJECTIVES

Intravenous polyvalent immunoglobulins (IVIG) for prophylaxis in patients with primary immunodeficiency disorders (PIDs) exposes them to life-threatening infections and debilitating diseases. To improve access to IVIG in lower middle-income countries, the WHO recommends a stepwise approach for the local production of purified and virus-inactivated plasma immunoglobulins by national blood transfusion services using new technologies and medical devices. One new technology relies on single-use sterile medical devices for the purification of plasma immunoglobulin G (IgG), as well as lipid-enveloped virus inactivation from mini-pools of recovered plasma separated from whole blood (mini-pool IVIG [MP-IVIG]). This study aimed to compare the safety and efficacy of MP-IVIG to standard IVIG (STD-IVIG).

MATERIALS AND METHODS

In this prospective crossover clinical study, we investigated the safety and efficacy of MP-IVIG for STD-IVIG preparations as a replacement therapy in a cohort of 21 paediatric patients with PID.

RESULTS

Both MP-IVIG and STD-IVIG were effective in reducing the frequency of severe bacterial infections and hospital admissions in patients with PID. Mild side effects have been observed in seven patients (6.2%) with PID who received MP-IVIG and five patients (5.3%) who received STD-IVIG. No moderate or severe side effects or haemolytic transfusion reactions were reported. The mortality rates were also comparable and were not related to the study products.

CONCLUSION

MP-IVIG presented no safety issues and was as effective as STD-IVIG in IgG replacement in patients with PID. Due to the small numbers, the results have to be addressed with caution.

Human inborn errors of immunity caused by defects of receptor and proteins of cellular membrane

Inborn errors of immunity are diseases of the immune system resulting from mutations that alter the expression of encoded proteins or molecules. Total updated number of these disorders is currently 406, with 430 different identified gene defects involved. Studies of the underlying mechanisms have contributed in better understanding the pathophysiology of the diseases, but also the complexity of the biology of innate and adaptive immune system and its interaction with microbes. In this review we present and briefly discuss Inborn Errors of Immunity caused by defects in genes encoding for receptors and protein of cellular membrane, including cytokine receptors, T cell antigen receptor (TCR) complex, cellular surface receptors or receptors signaling causing predominantly antibody deficiencies, co-stimulatory receptors and others. These alterations impact many biological processes of immune-system cells, including development, proliferation, activation and down-regulation of the immunological response, and result in a variety of diseases that present with distinct clinical features or with overlapping signs and symptoms.

"Immune TOR-opathies," a Novel Disease Entity in Clinical Immunology

Primary immunodeficiencies (PIDs) represent a group of mostly monogenic disorders caused by loss- or gain-of-function mutations in over 340 known genes that lead to abnormalities in the development and/or the function of the immune system. However, mutations in different genes can affect the same cell-signaling pathway and result in overlapping clinical phenotypes. In particular, mutations in the genes encoding for members of the phosphoinositide3-kinase (PI3K)/AKT/mTOR/S6 kinase (S6K) signaling cascade or for molecules interacting with this pathway have been associated with different PIDs that are often characterized by the coexistence of both immune deficiency and autoimmunity. The serine/threonine kinase mechanistic/mammalian target of rapamycin (mTOR), which acts downstream of PI3K and AKT, is emerging as a key regulator of immune responses. It integrates a variety of signals from the microenvironment to control cell growth, proliferation, and metabolism. mTOR plays therefore a central role in the regulation of immune cells’ differentiation and functions. Here, we review the different PIDs that share an impairment of the PI3K/AKT/mTOR/S6K pathway and we propose to name them “immune TOR-opathies” by analogy with a group of neurological disorders that has been originally defined by PB Crino and that are due to aberrant mTOR signaling (1). A better understanding of the role played by this complex intracellular cascade in the pathophysiology of “immune TOR-opathies” is crucial to develop targeted therapies.

Absent in Melanoma 2 (AIM2) limits pro-inflammatory cytokine transcription in cardiomyocytes by inhibiting STAT1 phosphorylation

Interferon (IFN)-γ is highly upregulated during heart inflammation and enhances the production of pro-inflammatory cytokines. Absent in Melanoma 2 (AIM2) is an IFN-inducible protein implicated as a component of the inflammasome. Here we seek to determine the role of AIM2 during inflammation in cardiac cells. We found that the presence of AIM2, but not of the other inflammasome components Nod-like receptor (NLR) NLRP3 or NLRC4, specifically limited the transcription of the pro-inflammatory cytokines interleukin (IL)-6, IP-10, and tumor necrosis factor (TNF)-α in HL-1 mouse cardiomyocytes stimulated with IFN-γ and lipopolysaccharides (LPS). Similarly, AIM2 reduced pro-inflammatory cytokine transcription in primary mouse neonatal cardiomyocytes (MNC), but not in primary mouse neonatal cardiac fibroblasts (MNF). Interestingly, AIM2-dependent reduction of pro-inflammatory cytokines in cardiomyocytes was independent of Caspase-1. Mechanistically, AIM2 reduced pro-inflammatory cytokine transcription in cardiomyocytes by interacting with and inhibiting the phosphorylation of STAT1. In AIM2-depleted cardiomyocytes, increased STAT1 phosphorylation enhanced the NF-κB pathway by promoting NF-κB p65 phosphorylation and acetylation. These results show for the first time that AIM2 plays an important anti-inflammatory, yet inflammasome-independent function in cardiomyocytes. Our findings will help to further understand how the various heart cell types differently react to inflammatory stimuli.

Effect of 90Sr internal emitter on gene expression in mouse blood

Background

The radioactive isotope Strontium-90 (⁹⁰Sr) may be released as a component of fallout from nuclear accidents, or in the event of a radiological incident such as detonation of an improvised nuclear device, and if ingested poses a significant health risk to exposed individuals. In order to better understand the response to ⁹⁰Sr, using an easily attainable and standard biodosimetry sample fluid, we analyzed the global transcriptomic response of blood cells in an in vivo model system.

Results

We injected C57BL/6 mice with a solution of 90SrCl2 and followed them over a 30-day period. At days 4, 7, 9, 25 and 30, we collected blood and isolated RNA for microarray analyses. These days corresponded to target doses in a range from 1–5 Gy. We investigated changes in mRNA levels using microarrays, and changes in specific microRNA (miRNA) predicted to be involved in the response using qRT-PCR. We identified 8082 differentially expressed genes in the blood of mice exposed to ⁹⁰Sr compared with controls. Common biological functions were affected throughout the study, including apoptosis of B and T lymphocytes, and atrophy of lymphoid organs. Cellular functions such as RNA degradation and lipid metabolism were also affected during the study. The broad down regulation of genes observed in our study suggested a potential role for miRNA in gene regulation. We tested candidate miRNAs, mmu-miR-16, mmu-miR-124, mmu-miR-125 and mmu-mir-21; and found that all were induced at the earliest time point, day 4.

Conclusions

Our study is the first to report the transcriptomic response of blood cells to the internal emitter ⁹⁰Sr in mouse and a possible role for microRNA in gene regulation after ⁹⁰Sr exposure. The most dramatic effect was observed on gene expression related to B-cell development and RNA maintenance. These functions were affected by genes that were down regulated throughout the study, suggesting severely compromised antigen response, which may be a result of the deposition of the radioisotope proximal to the hematopoietic compartment in bone.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1774-z) contains supplementary material, which is available to authorized users.

Molecular Diagnostic Challenges and Complex Management of Consecutive Twin Pregnancies in a Family with CD40 Ligand Deficiency

X-linked hyper-IgM syndrome (XHIGM) is a primary immunodeficiency disorder (PID) caused by mutation in the gene encoding the CD40 ligand (CD40L) expressed on activated T cells. Prenatal genotyping in carriers with twin pregnancies is more challenging than in women with singleton pregnancies. In addition, women with twin pregnancies may decide on selective termination for which the risk of loss of the healthy foetus may exceed 7%. We report here on a family affected by XHIGM. Diagnosis of the disease was made in a male patient as late as 33 years of age. After family screening, the sister of the proband conceived male twins in two consecutive pregnancies. In the first pregnancy, one of the male foetuses was hemizygous for the c.521A>G (Q174R) mutation in the CD40L gene. In the second pregnancy, ultrasound scan showed one foetus to have exencephaly and karyotyping revealed this foetus to have trisomy 18. Several options were discussed, but the parents decided on selective termination in both pregnancies. The interventions were successful in both cases, and the mother now has two healthy sons. This report demonstrates the way in which advanced technologies in molecular medicine and obstetric interventions may assist families with decisions about possible selective termination in case of life-threatening molecular or chromosomal disorders. Diagnosis of CD40L deficiency at the age of 33 years in the proband was striking and indicated that PIDs are still neglected as disease entities in the evaluation of patients with recurrent severe infectious diseases.

T cell immunodeficiency

T cell immunodeficiency can occur as one of a group of primary disorders or develop secondary to chronic infection, illness or drug therapy. Primary T cell disorders are rare, accounting for approximately 11% of reported primary immunodeficiencies, and generally present in infancy or early childhood. Early recognition is very important as many of these patients will require bone marrow transplantation prior to the onset of severe infection or other complications. Because of their rarity, these infants usually present to clinicians who have little or no prior experience of these conditions, and therefore laboratory-based clinicians with knowledge of the key laboratory/pathological abnormalities and clinical features have a valuable role in identifying the possibility of immunodeficiency. Secondary T cell deficiency is a cardinal feature of HIV infection and the specific susceptibility to infectious micro-organisms is highlighted. The possibility of T cell immunodeficiency should be considered in any patient presenting with unusual or severe viral, fungal or protozoal infection.

Classification of inflammatory skin diseases: a proposal based on the disorders of the three-layered defense systems, barrier, innate immunity and acquired immunity

The host defense system of the skin is composed of (1) a barrier, (2) innate immunity, and (3) acquired immunity. Inflammatory skin diseases can be classified into one of the disorders of these layers of the defense system, unless there is an ordinary response to specific infectious agents or internal/external injury. Any inflammatory skin disease partly simulates the response to real infections or dangers. Disorders of acquired immunity can be classified into (1) immunodeficiency, (2) immunohyperactivity (allergy), and (3) qualitative disorder (autoimmunity). Disorders of innate immunity can be classified into (1) innate immunodeficiency, (2) innate immunohyperactivity (general or local autoinflammation), and (3) qualitative disorder (general or local innate autoimmunity). The barrier of the skin is composed of (1) the physical barrier and (2) the chemical barrier. Several diseases, such as atopic dermatitis, are attributed to the disorder of these components of the barrier. Here, we propose an algorithm to classify the pathology of inflammatory skin diseases by means of what disorder in the specific layer of the host defense system is truly responsible.

Therapeutic management of primary immunodeficiency in older patients

Primary immunodeficiency disease (PID) has traditionally been viewed as a group of illnesses seen in the paediatric age group. New advances in diagnosis and treatment have led to an increase in the number of elderly PID patients. However, there is lack of research evidence on which to base clinical management in this group of patients. Management decisions often have to be based therefore on extrapolations from other patient cohorts or from younger patients. Data from the European Society for Immunodeficiencies demonstrates that the vast majority of elderly patients suffer from predominantly antibody deficiency syndromes. We review the management of PID disease in the elderly, with a focus on antibody deficiency disease.

Hypomorphic homozygous mutations in phosphoglucomutase 3 (PGM3) impair immunity and increase serum IgE levels

BACKGROUND

Recurrent bacterial and fungal infections, eczema, and increased serum IgE levels characterize patients with the hyper-IgE syndrome (HIES). Known genetic causes for HIES are mutations in signal transducer and activator of transcription 3 (STAT3) and dedicator of cytokinesis 8 (DOCK8), which are involved in signal transduction pathways. However, glycosylation defects have not been described in patients with HIES. One crucial enzyme in the glycosylation pathway is phosphoglucomutase 3 (PGM3), which catalyzes a key step in the synthesis of uridine diphosphate N-acetylglucosamine, which is required for the biosynthesis of N-glycans.

OBJECTIVE

We sought to elucidate the genetic cause in patients with HIES who do not carry mutations in STAT3 or DOCK8.

METHODS

After establishing a linkage interval by means of SNPchip genotyping and homozygosity mapping in 2 families with HIES from Tunisia, mutational analysis was performed with selector-based, high-throughput sequencing. Protein expression was analyzed by means of Western blotting, and glycosylation was profiled by using mass spectrometry.

RESULTS

Mutational analysis of candidate genes in an 11.9-Mb linkage region on chromosome 6 shared by 2 multiplex families identified 2 homozygous mutations in PGM3 that segregated with disease status and followed recessive inheritance. The mutations predict amino acid changes in PGM3 (p.Glu340del and p.Leu83Ser). A third homozygous mutation (p.Asp502Tyr) and the p.Leu83Ser variant were identified in 2 other affected families, respectively. These hypomorphic mutations have an effect on the biosynthetic reactions involving uridine diphosphate N-acetylglucosamine. Glycomic analysis revealed an aberrant glycosylation pattern in leukocytes demonstrated by a reduced level of tri-antennary and tetra-antennary N-glycans. T-cell proliferation and differentiation were impaired in patients. Most patients had developmental delay, and many had psychomotor retardation.

CONCLUSION

Impairment of PGM3 function leads to a novel primary (inborn) error of development and immunity because biallelic hypomorphic mutations are associated with impaired glycosylation and a hyper-IgE-like phenotype.

The spread of the J Project

The J Project physician education and clinical research collaboration program was launched in 2004 in Eastern and Central Europe (ECE). In less than 10 years, it has achieved remarkable success. This project aims to increase knowledge in the field of primary immunodeficiency disorders (PID), and to improve the diagnosis and treatment of patients worldwide, particularly in countries with limited economic resources, which currently report fewer such patients than expected. In most ECE countries, gene sequencing, which can provide a definitive diagnosis of PID, still remains unavailable. By contrast, such technology is used elsewhere to detect the more than 200 PID-causing genes that have been discovered in the last three decades. Thus, PID awareness programs like the J Project remain critically important, to improve diagnostic facilities and treatment and to promote clinical research collaboration. This paper highlights the achievements of the J Project and the spread of its concepts and spirit to the countries of Western Asia.

Molecular mechanisms of mucocutaneous immunity against Candida and Staphylococcus species

Signal transducer and activator of transcription (STAT) proteins are key components of the innate and adaptive immune responses to pathogenic microorganisms. Recent research on primary immunodeficiency disorders and the identification of patients carrying germline mutations in STAT1, STAT3, and STAT5B have highlighted the role of human STATs in host defense against various viruses, bacteria, and fungi. Mutations in STAT1 and STAT3 disrupt various cytokine pathways that control mucocutaneous immunity against Candida species, especially Candida albicans, and Staphylococcus species, especially Staphylococcus aureus. Here we consider inborn errors of immunity arising from mutations in either STAT1 or STAT3 that affect mucocutaneous immunity to Candida and Staphylococcus species.

The prevalences [correction] and patient characteristics of primary immunodeficiency diseases in Turkey--two centers study

PURPOSE

Primary immunodeficiency diseases (PIDs) are inherited disorders of the immune system resulting in increased susceptibility to unusual infections and predisposition to autoimmunity and malignancies. The European Society for Immunodeficiencies (ESID) has developed an internet-based database for clinical and research data on patients with PID. This study aimed to provide a minimum estimate of the prevalence of each disorder and to determine the clinical characteristics and outcomes of patients with PID in Turkey.

METHODS

Clinical features of 1435 patients with primary immunodeficiency disorders are registered in ESID Online Patient Registry by the Pediatric Immunology Departments of the Medical Faculties of Uludag University and Ege University Between 2004 and 2010. These two centers are the major contributors reporting PID patients to ESID database from Turkey.

RESULTS

Predominantly antibody immunodeficiency (73.5 %) was the most common category followed by autoinflammatory disorders (13.3 %), other well defined immunodeficiencies (5.5 %), congenital defects of phagocyte number, function or both 3.5 %), combined T and B cell immunodeficiencies (2 %), defects in innate immunity (1 %), and diseases of immune dysregulation (0.7 %). Patients between 0 and 18 years of age constitued 94 % of total and the mean age was 9.2 ± 6 years. The consanguinity rate within the registered patients was 14.3 % (188 of 1130 patients). The prevalance of all PID cases ascertained from the registry was 30.5/100.000. The major cause of the mortality was severe infection which was seen in forty-two of seventy five deceased patients. The highest mortality was observed in patients with severe combined immunodeficiencies and ataxia-telangiectasia.

CONCLUSION

Promoting the awareness of PID among the medical professionals and the general public is required if premature death and serious morbidity occurs due to late diagnosis of the wider spectrum of PID are to be avoided.

Primary immunodeficiencies in highly consanguineous North African populations

The study of inbred populations has contributed remarkably to the description of new autosomal recessive primary immunodeficiencies (PIDs). Here, we examine the pattern of PIDs in North African populations and assess the impact of highly prevalent consanguinity. This review reports on the current status of pediatricians' awareness of PIDs in Egypt, Morocco, and Tunisia, where awareness of PIDs is relatively recent. The phenotypic distribution of PIDs is reported and compared among the three countries and with other populations. Data analysis reveals a prevalence of autosomal recessive forms and a peculiar distribution of major PID categories, particularly more combined immunodeficiencies than antibody disorders. In these endogamous communities, molecular diagnosis is critical to developing a genetic-based preventive approach. The organization of diagnosis and care services in these resource-limited settings faces many obstacles. Autosomal recessive PIDs are overrepresented; thus, it is critical to continue investigation of these diseases in order to better understand the underlying mechanisms and to improve patient care.

Primary immune deficiency disorders in the South Pacific: the clinical utility of a customized genetic testing program in New Zealand

Primary immune deficiency disorders (PIDs) are a group of diseases associated with a genetic susceptibility to recurrent infections, malignancy, autoimmunity, and allergy. The molecular basis of many of these disorders has been identified in the last two decades. Most are inherited as single gene defects. As discussed in this paper, identifying the underlying genetic defect plays a critical role in many areas-including patient management, diagnosis, identifying atypical presentations, family studies, providing prognostic information, prenatal diagnosis, and defining new diseases. New Zealand is a geographically isolated, developed country in the South Pacific. We have introduced a dedicated customized genetic testing service for PID patients in New Zealand. This accredited diagnostic program offers rapid turnaround times for genetic tests and minimizes the risk of laboratory errors. Here we review the clinical indications for genetic testing for PIDs based on cases referred to the molecular immunology diagnostic service at Auckland City Hospital.

Epigenomic deregulation in the immune system

Proper immune function is the result of multiple cell commitment and differentiation steps, and adequate control of activation mechanisms. Deregulation of transcriptional programs in immune cells leads to the development of hematological malignancies, autoimmune diseases or immunodeficiencies. In this sense, epigenetic control of gene expression plays an essential role in the correct function of the immune system and the integrity of identity of relevant cell types. Epigenetic deregulation can result as a consequence of genetic changes in transcription factors, elements of signaling pathways or epigenetic enzymes, or as an effect of a variety of environmental factors. On top of genetic predisposition, viral infection and other external factors influence the development of immune-related diseases. In recent years, major strides have been made towards understanding the contribution of genetics in these immune disorders. Less progress has been made in dissecting the contribution of epigenetic factors in their etiology. Herein, it is presented what is currently known about epigenetic alterations in immune system associated disorders. It is also discussed how epigenomic analysis can help to understand the molecular basis of these diseases and how this information can be used in the clinical setting.

Clinical features that identify children with primary immunodeficiency diseases

BACKGROUND

The 10 warning signs of primary immunodeficiency diseases (PID) have been promoted by various organizations in Europe and the United States to predict PID. However, the ability of these warning signs to identify children with PID has not been rigorously tested.

OBJECTIVE

The main goal of this study was to determine the effectiveness of these 10 warning signs in predicting defined PID among children who presented to 2 tertiary pediatric immunodeficiency centers in the north of England.

METHODS

A retrospective survey of 563 children who presented to 2 pediatric immunodeficiency centers was undertaken. The clinical records of 430 patients with a defined PID and 133 patients for whom detailed investigations failed to establish a specific PID were reviewed.

RESULTS

Overall, 96% of the children with PID were referred by hospital clinicians. The strongest identifiers of PID were a family history of immunodeficiency disease in addition to use of intravenous antibiotics for sepsis in children with neutrophil PID and failure to thrive in children with T-lymphocyte PID. With these 3 signs, 96% of patients with neutrophil and complement deficiencies and 89% of children with T-lymphocyte immunodeficiencies could be identified correctly. Family history was the only warning sign that identified children with B-lymphocyte PID.

CONCLUSIONS

PID awareness initiatives should be targeted at hospital pediatricians and families with a history of PID rather than the general public. Our results provide the general pediatrician with a simple refinement of 10 warning signs for identifying children with underlying immunodeficiency diseases.

Nijmegen breakage syndrome complicated with primary cutaneous tuberculosis

Nijmegen breakage syndrome (NBS) is a rare autosomal recessive chromosomal instability syndrome characterized by severe immunodeficiency, growth retardation, microcephaly, a distinct facial appearance, and a high predisposition to lymphoid malignancy. We report a 7-year-old white girl with NBS associated with cutaneous tuberculosis. The patient presented with multiple red-brown, centrally scaring plaques on the leg and had neither pulmonary nor systemic manifestation of tuberculosis. Polymerase chain reaction testing using Mycobacterium genus- and Mycobacterium tuberculosis species-specific primers confirmed the clinical diagnosis of cutaneous tuberculosis. This is the first report describing the simultaneous presentation of NBS and cutaneous tuberculosis.

Transient glutathione depletion determines terminal differentiation in HL-60 cells

To better define the role of glutathione (GSH) in cell differentiation, the present study measured GSH concentrations during terminal HL-60 cell differentiation, in the presence and absence of differentiation-inducing agents, and in the presence and absence of GSH altering agents. Interestingly, there was a small transient increase in intracellular GSH levels during dimethyl sulfoxide (DMSO) or 1α,25-dihydroxyvitamin D3 (VD3) induced differentiation. This increase coincided with an increase in nitroblue tetrazolium (NBT) reduction capacity, a measure of superoxide anion production, but there was no apparent change in the GSH/glutathione disulfide (GSSG) ratio. Surprisingly, treatment of cells with low doses of 1-chloro-2,4-dinitrobenzene (CDNB; 5 µM) or diethylmaleate (DEM; 0.5 mM), which transiently deplete GSH levels to about 40% of control levels, resulted in enhanced differentiation of HL-60 cells exposed to VD3 or all-trans-retinoic acid (ATRA), as well as under un-induced conditions (i.e., spontaneous differentiation). Enhanced differentiation occurred when cells were treated with the GSH-depleting agents 4 hours after treatment with differentiation inducers. These findings indicate that intracellular GSH levels are regulated in a complex fashion during HL-60 cell differentiation, and that transient GSH depletion using low doses of CDNB and DEM enhances the differentiation process.

Genetic characteristics of eighty-seven patients with the Wiskott-Aldrich syndrome

The Wiskott-Aldrich syndrome (WAS) is an X-linked recessive immune deficiency disorder characterized by thrombocytopenia, small platelet size, eczema, recurrent infections, and increased risk of autoimmune disorders and malignancies. WAS is caused by mutations in the WASP gene which encodes WASP, a 502-amino acid protein. WASP plays a critical role in actin cytoskeleton organization and signalling, and functions of immune cells. We present here the results of genetic analysis of patients with WAS from eleven Eastern and Central European (ECE) countries and Turkey. Clinical and haematological information of 87 affected males and 48 carrier females from 77 WAS families were collected. The WASP gene was sequenced from genomic DNA of patients with WAS, as well as their family members to identify carriers. In this large cohort, we identified 62 unique mutations including 17 novel sequence variants. The mutations were scattered throughout the WASP gene and included single base pair changes (17 missense and 11 nonsense mutations), 7 small insertions, 18 deletions, and 9 splice site defects. Genetic counselling and prenatal diagnosis were applied in four affected families. This study was part of the J Project aimed at identifying genetic basis of primary immunodeficiency disease in ECE countries. This report provides the first comprehensive overview of the molecular genetic and demographic features of WAS in ECE.

The clinical utility of molecular diagnostic testing for primary immune deficiency disorders: a case based review

Primary immune deficiency disorders (PIDs) are a group of diseases associated with a genetic predisposition to recurrent infections, malignancy, autoimmunity and allergy. The molecular basis of many of these disorders has been identified in the last two decades. Most are inherited as single gene defects. Identifying the underlying genetic defect plays a critical role in patient management including diagnosis, family studies, prognostic information, prenatal diagnosis and is useful in defining new diseases. In this review we outline the clinical utility of molecular testing for these disorders using clinical cases referred to Auckland Hospital. It is written from the perspective of a laboratory offering a wide range of tests for a small developed country.

Thymus microenvironment in human primary immunodeficiency diseases

PURPOSE OF REVIEW

Severe combined immunodeficiencies represent a heterogeneous group of genetic disorders affecting genes of both early and late steps in lymphocytes development, a process tightly controlled by thymic epithelial cells. Detailed analysis of thymic morphology aids to the assessment of the severity of the immune disorder and may be critical to the understanding of the role of the genetic defects in the pathophysiology of these diseases. In this review, we highlight recent advancements in the characterization of the thymic microenvironment in primary immunodeficiencies.

RECENT FINDINGS

Crosstalk between thymocytes and thymic epithelial cells is essential to preserve thymic architecture and function, and therefore to promote T-cell maturation and development of self-tolerance. Early severe defects in T-cell development result in profound abnormalities of thymic epithelial cells differentiation with loss of AIRE expression and severe reduction of thymic dendritic and T-regulatory cells. Differently, later defects in T-cell development that are permissive for normal thymocytes development allow cortico-medullary differentiation with partially preserved AIRE expression and dendritic/T-regulatory cells distribution. Hypomorphic mutations in the same genes partially permissive to T-cell development may result in a more complex phenotype with immunodysreactivity and peculiar thymic alterations.

SUMMARY

Although the molecular and genetic bases of primary immunodeficiencies directly aid to both diagnosis and management of the patients, the detailed analysis of thymic morphology critically contributes to unveil the pathophysiology of these diseases.

Bioinformatics services related to diagnosis of primary immunodeficiencies

PURPOSE OF REVIEW

Most primary immunodeficiencies (PIDs) have overlapping signs and symptoms - presenting a challenge for diagnosis. The information available from the Internet for over 200 PIDs is scattered between numerous services and databases. Patient information has been collected in different patient registries. Several software tools have been developed in order to build the databases, expert systems and other information systems useful in diagnosis or prediction.

RECENT FINDINGS

Previously released services have been significantly improved and some new bioinformatics tools have been developed to help in diagnosis, prediction, mutation analysis and classification of PIDs. Several national initiatives have been launched for centralized PID information services. The very latest additions are tools and approaches for PID candidate gene prioritization, systematic classification and a medical expert system to help in diagnosis.

SUMMARY

Many bioinformatics tools for PIDs are already freely available over the Internet. We expect bioinformatics tools to further help healthcare professionals in diagnosis, analysis and prediction. Currently, most of the resources are stand-alone and thus their integration will be a challenge for the future. Another challenge is to develop terminologies, ontologies and standards to achieve semantic interoperability.

Primary immunodeficiencies of protective immunity to primary infections

The vast majority of primary immunodeficiencies (PIDs) predispose affected individuals to recurrent or chronic infectious diseases, because they affect protective immunity to both primary and secondary or latent infections. We discuss here three recently described groups of PIDs that seem to impair immunity to primary infections without compromising immunity to secondary and latent infections. Patients with mutations in IL12B or IL12RB1 typically present mycobacterial disease in childhood with a favorable progression thereafter. Cross-protection between mycobacterial infections has even been observed. Patients with mutations in IRAK4 or MYD88 suffer from pyogenic bacterial diseases, including invasive pneumococcal diseases in particular. These diseases often recur, although not always with the same serotype, but the frequency of these recurrences tails off, with no further infections observed from adolescence onwards. Finally, mutations in UNC93B1 and TLR3 are associated with childhood herpes simplex encephalitis, which strikes only once in most patients, with almost no recorded cases of more than two bouts of this disease. Unlike infections in patients with other PIDs, the clinical course of which typically deteriorates with age even if appropriate treatment is given, the prognosis of patients with these three newly described PIDs tends to improve spontaneously with age, provided, of course, that the initial infection is properly managed. In other words, although life-threatening in early childhood, these new PIDs are associated with a favorable outcome in adulthood. They provide proof-of-principle that infectious diseases of childhood striking only once may result from single-gene inborn errors of immunity.

SLAM family receptors and the SLAM-associated protein (SAP) modulate T cell functions

One or more of the signaling lymphocytic activation molecule (SLAM) family (SLAMF) of cell surface receptors, which consists of nine transmembrane proteins, i.e., SLAMF1-9, are expressed on most hematopoietic cells. While most SLAMF receptors serve as self-ligands, SLAMF2 and SLAMF4 use each other as counter structures. Six of the receptors carry one or more copies of a unique intracellular tyrosine-based switch motif, which has high affinity for the single SH2-domain signaling molecules SLAM-associated protein and EAT-2. Whereas SLAMF receptors are costimulatory molecules on the surface of CD4+, CD8+, and natural killer (NK) T cells, they also involved in early phases of lineage commitment during hematopoiesis. SLAMF receptors regulate T lymphocyte development and function and modulate lytic activity, cytokine production, and major histocompatibility complex-independent cell inhibition of NK cells. Furthermore, they modulate B cell activation and memory generation, neutrophil, dendritic cell, macrophage and eosinophil function, and platelet aggregation. In this review, we will discuss the role of SLAM receptors and their adapters in T cell function, and we will examine the role of these receptors and their adapters in X-linked lymphoproliferative disease and their contribution to disease susceptibility in systemic lupus erythematosus.

Bone marrow transplantation for primary immunodeficiency diseases

Advances in immunology have led to a breathtaking expansion of recognized primary immunodeficiency diseases (PID) with over 120 disease-related genes identified. In North America alone more than 1000 children have received allogeneic blood or marrow transplant over the past 30 years, with the majority surviving long term. This review presents results and highlights challenges and notable advances, including novel less toxic conditioning regimens, to transplant the more common and severe forms of PID. HLA-matched sibling donors remain the ideal option, however, advances in living donor unrelated HSCT and banked umbilical cord blood grafts provide hope for all children with severe PID.

Novel primary immunodeficiencies relevant to internal medicine: novel phenotypes

Primary immunodeficiencies (PIDs) are often recognized in adults, either because of delayed diagnosis of a paediatric illness, or increasingly because of the recognition of adult onset forms of these diseases. Moreover, a growing fraction of children diagnosed with PIDs reach adulthood. It has become clear that many of these conditions affect various organs and therefore will be referred to professionals from various fields of internal medicine. It is well known that infectious diseases, allergy, auto-immunity and cancer may result from PIDs. Surprisingly, other clinical manifestations were recently found to reflect inborn errors of immunity. Ground-breaking discoveries suggest that atypical haemolytic uraemic syndrome, Crohn's disease, and alveolar proteinosis may actually be manifestations of novel PIDs.

Prediction of candidate primary immunodeficiency disease genes using a support vector machine learning approach

Screening and early identification of primary immunodeficiency disease (PID) genes is a major challenge for physicians. Many resources have catalogued molecular alterations in known PID genes along with their associated clinical and immunological phenotypes. However, these resources do not assist in identifying candidate PID genes. We have recently developed a platform designated Resource of Asian PDIs, which hosts information pertaining to molecular alterations, protein-protein interaction networks, mouse studies and microarray gene expression profiling of all known PID genes. Using this resource as a discovery tool, we describe the development of an algorithm for prediction of candidate PID genes. Using a support vector machine learning approach, we have predicted 1442 candidate PID genes using 69 binary features of 148 known PID genes and 3162 non-PID genes as a training data set. The power of this approach is illustrated by the fact that six of the predicted genes have recently been experimentally confirmed to be PID genes. The remaining genes in this predicted data set represent attractive candidates for testing in patients where the etiology cannot be ascribed to any of the known PID genes.

Helping the helpers!

T follicular helper (Tfh) cells are crucial for generating humoral immune responses. In this issue of Immunity, Schmitt et al. (2009) reveal the differentiation of human Tfh cells is dependent on dendritic cell-derived interleukin-12.

Primary immune deficiencies affecting lymphocyte differentiation: lessons from the spectrum of resulting infections

Understanding primary immunodeficiencies has elucidated many aspects of human immunity and susceptibility to infections. Recently, defects have been identified that result in deficiencies of terminally differentiated subsets of lymphocytes including deficiencies of memory B cells, NKT cells and T(h)17 T cells. Together with defects specific to T(h)1 responses, these disorders revealed that dedicated pathogen-specific mechanisms exist for prevalent human pathogens, and that some host defence strategies are remarkably specific. Deficiency of T(h)17 cells confirms that this subset of effector T cells is important for defence at epithelial surfaces. The clinical phenotype includes devastating complications from infection with Staphylococcus aureus. Since the microbial load at human epithelial surfaces is substantial and enormously diverse, this specificity could hold clues that are important for understanding first the complex symbiosis with mucosal commensals and second for understanding the consequences of manipulating these populations in inflammatory diseases.

New approaches to treatment of primary immunodeficiencies: fixing mutations with chemicals

PURPOSE OF REVIEW

This review is to highlight the most current mutation-targeted therapeutic approaches and provide insights into new developments for treating primary immunodeficiencies.

RECENT FINDINGS

Significant progress in mutation-targeted treatment was achieved in the past year with the identification and characterization of a translational read-through compound, PTC124. PTC124 demonstrates a new class of nontoxic bioavailable small drugs. Antisense oligonucleotide-mediated techniques such as splicing redirection, exon skipping, and mismatch repair have been successfully used to correct splicing, frameshift, and missense mutations, respectively. Delivery of antisense oligonucleotides to mammalian cells, including primary leukocytes and neurons, saw great progress during the past year. Recent advances for other approaches to correct frameshift and missense mutations are also considered.

SUMMARY

Primary immunodeficiencies are monogenic disorders. The characterization and classification of disease-causing mutations facilitate the design and development of new mutation-targeted treatments. To date, using ataxia-telangiectasia (A-T) as a model primary immunodeficiency, the most promising advances have been with chemicals that read through various premature stop codons as well as with antisense oligonucleotides that mask aberrant splice sites. These principles can now be applied to other primary immunodeficiencies.

Optimization of immunoglobulin substitution therapy by a stochastic immune response model

Background

The immune system is a complex adaptive system of cells and molecules that are interwoven in a highly organized communication network. Primary immune deficiencies are disorders in which essential parts of the immune system are absent or do not function according to plan. X-linked agammaglobulinemia is a B-lymphocyte maturation disorder in which the production of immunoglobulin is prohibited by a genetic defect. Patients have to be put on life-long immunoglobulin substitution therapy in order to prevent recurrent and persistent opportunistic infections.

Methodology

We formulate an immune response model in terms of stochastic differential equations and perform a systematic analysis of empirical therapy protocols that differ in the treatment frequency. The model accounts for the immunoglobulin reduction by natural degradation and by antigenic consumption, as well as for the periodic immunoglobulin replenishment that gives rise to an inhomogeneous distribution of immunoglobulin specificities in the shape space. Results are obtained from computer simulations and from analytical calculations within the framework of the Fokker-Planck formalism, which enables us to derive closed expressions for undetermined model parameters such as the infection clearance rate.

Conclusions

We find that the critical value of the clearance rate, below which a chronic infection develops, is strongly dependent on the strength of fluctuations in the administered immunoglobulin dose per treatment and is an increasing function of the treatment frequency. The comparative analysis of therapy protocols with regard to the treatment frequency yields quantitative predictions of therapeutic relevance, where the choice of the optimal treatment frequency reveals a conflict of competing interests: In order to diminish immunomodulatory effects and to make good economic sense, therapeutic immunoglobulin levels should be kept close to physiological levels, implying high treatment frequencies. However, clearing infections without additional medication is more reliably achieved by substitution therapies with low treatment frequencies. Our immune response model predicts that the compromise solution of immunoglobulin substitution therapy has a treatment frequency in the range from one infusion per week to one infusion per two weeks.

Genetic syndromic immunodeficiencies with antibody defects

This article reviews the major syndromic immunodeficiencies with significant antibody defects, many of which may require intravenous immunogammaglobulin therapy. The authors define syndromic immunodeficiency as an illness associated with a characteristic group of phenotypic abnormalities or laboratory features that comprise a recognizable syndrome. Many are familial with a defined inheritance pattern. Immunodeficiency may not be a major part of the illness and may not be present in all patients; thus, these conditions differ from primary immunodeficiency syndromes, in which immune abnormalities are a consistent and prominent feature of their disease.

The genetic heterogeneity of mendelian susceptibility to mycobacterial diseases

Primary immunodeficiencies (PIDs) were long thought to be exclusively recessive traits -- autosomal recessive (AR) in most cases, with a few X-linked recessive (XR) diseases. In recent years, autosomal dominant (AD), mitochondrial, polygenic, and even somatic PIDs have been described. However, AR remains the most frequent inheritance pattern among recently described PIDs. Some PIDs have been shown to be genetically heterogeneous. Mendelian susceptibility to mycobacterial diseases (MSMD) displays a high level of genetic heterogeneity. There are 6 MSMD-causing genes, including 1 X-linked gene (nuclear factor-kappaB-essential modulator [NEMO]) and 5 autosomal genes (IFN-gamma receptor 1 [IFNGR1], IFN-gamma receptor 2 [IFNGR2], signal transducer and activator of transcription 1 [STAT1], IL-12 p40 subunit [IL12P40], and IL-12 receptor beta-subunit [IL12RB1]). The X-linked trait is XR; STAT1 deficiency is AD; the IFNGR2, IL12P40 subunit, and IL12RB1 deficiencies are AR; and IFNGR1 deficiency may be AD or AR. Two of the AR traits (IFNGR1, IFNGR2) may be subdivided into complete and partial deficiencies, and 3 AR complete deficiencies (IFNGR1, IFNGR2, IL12RB1) may be subdivided into disorders with and without cell surface expression. Finally, there are 2 types of AD STAT1 deficiency, depending on whether the mutation impairs phosphorylation or DNA binding. Thirteen genetic disorders conferring MSMD have been described, involving 1 XR, 3 AD (2 genes), and 9 AR traits (4 genes). However, no genetic etiology has yet been identified for about half of all patients with MSMD. We expect to identify new XR and AD causes of MSMD, but new AR etiologies of MSMD are also likely to be discovered. The investigation of children from areas in which consanguineous marriages are common will probably facilitate the description of many more AR traits.

Identification of candidate disease genes by integrating Gene Ontologies and protein-interaction networks: case study of primary immunodeficiencies

Disease gene identification is still a challenge despite modern high-throughput methods. Many diseases are very rare or lethal and thus cannot be investigated with traditional methods. Several in silico methods have been developed but they have some limitations. We introduce a new method that combines information about protein-interaction network properties and Gene Ontology terms. Genes with high-calculated network scores and statistically significant gene ontology terms based on known diseases are prioritized as candidate genes. The method was applied to identify novel primary immunodeficiency-related genes, 26 of which were found. The investigation uses the protein-interaction network for all essential immunome human genes available in the Immunome Knowledge Base and an analysis of their enriched gene ontology annotations. The identified disease gene candidates are mainly involved in cellular signaling including receptors, protein kinases and adaptor and binding proteins as well as enzymes. The method can be generalized for any disease group with sufficient information.

Basal and stimulus-induced cytokine expression is selectively impaired in peripheral blood mononuclear cells of newborn foals

Neonates are thought to be generally deficient in production of Th-1-associated cytokines at birth, and thereby more susceptible to bacterial infections. Using neonatal foals as a model, this study examined the age-dependent maturation of both basal and stimulus-induced immune responses, as reflected by the expression of a panel of Th-1-associated and pro-inflammatory cytokines. Results showed that although the basal production of IFN-gamma and IL-6 was impaired (P<0.05) in PBMCs of neonatal foals at birth, the basal production of IL-8, IL-12(p35/p40) and IL-23(p19/p40) were either in excess of or comparable to that of older foals. In response to Rhodococcus equi and CpG-ODN stimulation in vitro, PBMCs of neonatal foals showed increased (P<0.05) expression of IFN-gamma and IL-6, and preferentially increased expression of either IL-23(p19/p40) with R. equi stimulation or IL-12(p35/p40) with CpG-ODN stimulation. The magnitude of these stimulus-induced responses (except for IL-23p19), were significantly (P<0.05) less for newborn foals than for older foals. The selective impairment of age-dependent basal and stimulus-induced cytokine expression by newborn foals may reflect the different functional state of various TLR pathways in newborns, and be directly associated with their age-dependent susceptibility to infection. Our results indicate that CpG-ODNs can selectively stimulate deficient cytokines (P<0.05) from PBMCs in newborn foals in vitro, suggesting immunoprophylactic or therapeutic potential of CpG-ODNs.