Beyond APECED: An update on the role of the autoimmune regulator gene (AIRE) in physiology and disease

AIRE Deficiency Leads to the Development of Alopecia Areata‒Like Lesions in Mice

Alopecia areata (AA) is an autoimmune hair loss disorder with no cure. Patients with sequence variation in AIRE are 15 times more likely to develop AA than the general population, yet the roles of AIRE in AA pathogenesis are unknown. In this study, we report that 62% of C57BL/6J female Aire^‒/‒ mice spontaneously developed persistent AA-like lesions that displayed several hallmarks of human AA. Lesional Aire^‒/‒ skin exhibited hair follicle (HF) dystrophy as determined by a reduced number of anagen HFs, decreased anagen HF proliferation, hair pigmentary changes, and decreased hair width and length. Inflammatory infiltrate comprising CD8⁺ T cells, CD4⁺ T cells, CD68⁺ macrophages, and mast cells was prominent in lesional Aire^‒/‒ HFs. From gene expression analyses, we found lesional Aire^‒/‒ skin to have significantly increased expression of human AA signature genes, including H2-Ab1, Ifnγ, IFN-γ‒induced chemokines (Ccl5, Cxcl9‒11), γ_c family cytokine receptor Il2RA, and JAK‒signal transducer and activator of transcription (STAT) signaling components (Stat1, Stat2, Stat4). By immunostaining, lesional Aire^‒/‒ HFs also show upregulated major histocompatibility complex class I and downregulated α-melanocyte-stimulating hormone, signifying immune privilege collapse, and increased STAT1 activation in HF keratinocytes. Our study highlights a role for AIRE in HF biology and shows that Aire^‒/‒ mice may serve as a valuable model system to study AA pathogenesis.

Extrathymic AIRE-expressing cells: Friends or foes in autoimmunity and cancer?

Auto-immune regulator (AIRE) is a transcription factor that is mainly known for its crucial role in the thymus. Here, AIRE ensures central tolerance by promoting the expression of peripheral tissue antigens in thymic epithelial cells, which is essential for the negative selection of autoreactive T cells. Intriguingly, AIRE expressing cells have recently been identified in other tissues outside the thymus as well. However, the exact function of these extrathymic AIRE expressing cells (eTACs) remains largely enigmatic. Human eTACs are mainly found in secondary lymphoid tissues under homeostatic conditions, but are also found in pathologies such as the inflamed tissues of patients with autoimmune diseases and in various cancer tissues. eTACs have been demonstrated to express dendritic cell (DC)-like markers, such as MHCII, CD40 and CD127, but also CCR7, IDO and PD-L1. Interestingly, eTACs lack high expression of co-stimulatory molecules, such as CD80 or CD86. In mice, different types of peripheral AIRE expressing cells have been described, including cells with an innate lymphoid cell-like phenotype and antigen presenting cell (APC) function. These findings suggest that eTACs are APCs with the possibility to modulate or inhibit immune responses, which is confirmed by functional murine studies demonstrating the ability of eTACs to induce tolerance in autoreactive T cells. The potential immunomodulatory function of eTACs makes them promising targets to restore tolerance in autoimmunity or improve immunotherapy in cancer settings. Yet, this requires a better understanding of these cells and the molecular mechanisms involved. In this review we aim to summarize the current knowledge and understanding of eTACs, including their putative roles in health and disease.

Beyond the marks: reader-effectors as drivers of epigenetics and chromatin engineering

Chromatin is a system of proteins and DNA that regulates chromosome organization and gene expression in eukaryotes. Essential features that support these processes include biochemical marks on histones and DNA, 'writer' enzymes that generate or remove these marks and proteins that translate the marks into transcriptional regulation: reader-effectors. Here, we review recent studies that reveal how reader-effectors drive chromatin-mediated processes. Advances in proteomics and epigenomics have accelerated the discovery of chromatin marks and their correlation with gene states, outpacing our understanding of the corresponding reader-effectors. Therefore, we summarize the current state of knowledge and open questions about how reader-effectors impact cellular function and human disease and discuss how synthetic biology can deepen our knowledge of reader-effector activity.

Generation and Characterization of iPS Cells Derived from APECED Patients for Gene Correction

APECED (Autoimmune-Polyendocrinopathy-Candidiasis-Ectodermal-Dystrophy) is a severe and incurable multiorgan autoimmune disease caused by mutations in the AIRE (autoimmune regulator) gene. Without functional AIRE, the development of central and peripheral immune tolerance is severely impaired allowing the accumulation of autoreactive immune cells in the periphery. This leads to multiple endocrine and non-endocrine autoimmune disorders and mucocutaneous candidiasis in APECED patients. Recent studies have suggested that AIRE also has novel functions in stem cells and contributes to the regulatory network of pluripotency. In preparation of therapeutic gene correction, we generated and assessed patient blood cell-derived iPSCs, potentially suitable for cell therapy in APECED. Here, we describe APECED-patient derived iPSCs's properties, expression of AIRE as well as classical stem cell markers by qPCR and immunocytochemistry. We further generated self-aggregated EBs of the iPSCs. We show that APECED patient-derived iPSCs and EBs do not have any major proliferative or apoptotic defects and that they express all the classical pluripotency markers similarly to healthy person iPSCs. The results suggest that the common AIRE R257X truncation mutation does not affect stem cell properties and that APECED iPSCs can be propagated in vitro and used for subsequent gene-correction. This first study on APECED patient-derived iPSCs validates their pluripotency and confirms their ability for differentiation and potential therapeutic use.

Nobel Prize for immune checkpoint inhibitors, understanding the immunological switching between immunosuppression and autoimmunity

INTRODUCTION

Immune checkpoint inhibitors (ICIs) are a revolutionary form of immunotherapy in cancer. However, the percentage of patients responding to therapy is relatively low, while adverse effects occur in a large number of patients. In addition, the therapeutic mechanisms of ICIs are not yet completely described.

AREAS COVERED

The initial view (articles published in PubMed, Scopus, Web of Science, etc.) was that ICIs increase tumor-specific immunity. Recent data (collected from the same databases) suggest that the ICIs pharmacotherapy actually extends beyond the topic of immune reactivity, including additional immune pathways, such as disrupting immunosuppression and increasing tumor-specific autoimmunity. Unfortunately, there is no clear delimitation between these specific autoimmune reactions that are therapeutically beneficial, and nonspecific autoimmune reactions/toxicity that can be extremely severe side effects.

EXPERT OPINION

Immune checkpoint mechanisms perform a non-selective immune regulation, maintaining a dynamic balance between immunosuppression and autoimmunity. By blocking these mechanisms, ICIs actually perform an immunological reset, decreasing immunosuppression and increasing tumor-specific immunity and predisposition to autoimmunity. The predisposition to autoimmunity induces both side effects and beneficial autoimmunity. Consequently, further studies are necessary to maximize the beneficial tumor-specific autoimmunity, while reducing the counterproductive effect of associated autoimmune toxicity.

Sjögren's syndrome: a systemic autoimmune disease

Sjögren's syndrome is a chronic autoimmune disease characterized by ocular and oral dryness resulting from lacrimal and salivary gland dysfunction. Besides, a variety of systemic manifestations may occur, involving virtually any organ system. As a result, the disease is characterized by pleomorphic clinical manifestations whose characteristics and severity may vary greatly from one patient to another. Sjögren's syndrome can be defined as primary or secondary, depending on whether it occurs alone or in association with other systemic autoimmune diseases, respectively. The pathogenesis of Sjögren's syndrome is still elusive, nevertheless, different, not mutually exclusive, models involving genetic and environmental factors have been proposed to explain its development. Anyhow, the emergence of aberrant autoreactive B-lymphocytes, conducting to autoantibody production and immune complex formation, seems to be crucial in the development of the disease. The diagnosis of Sjögren's syndrome is based on characteristic clinical signs and symptoms, as well as on specific tests including salivary gland histopathology and autoantibodies. Recently, new classification criteria and disease activity scores have been developed primarily for research purposes and they can also be useful tools in everyday clinical practice. Treatment of Sjögren's syndrome ranges from local and symptomatic therapies aimed to control dryness to systemic medications, including disease-modifying agents and biological drugs. The objective of this review paper is to summarize the recent literature on Sjögren's syndrome, starting from its pathogenesis to current therapeutic options.

Late-onset autoimmune polyendocrine syndrome type 1: a case report and literature review

Autoimmune polyendocrine syndrome type 1 (APS-1), also referred to as autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED), a rare monogenic disorder, is classically characterized by a triad of chronic mucocutaneous candidiasis, hypoparathyroidism, and primary adrenal insufficiency. The identified causative gene is autoimmune regulator (AIRE), which encodes a critical transcription factor and is essential for self-tolerance. Here, we describe a late-onset Chinese case who presented with symptoms of persistent tetany due to hypocalcemia. Extensive clinical evaluations revealed that the patient manifested beyond the classic triad of the disease, and next-generation sequencing identified a known homozygous AIRE mutation (p.R139X). APS-1 is a rare inherited immunodeficiency disease with high clinical and genetic heterogeneity. By retrospectively analyzing the disease, we comprehensively reviewed the phenotypic features, summarized the genotype spectrum, and discussed the possible immunological mechanisms of the disease to enhance earlier recognition and implement targeted preventive and therapeutic strategies.

What can clinical immunology learn from inborn errors of epigenetic regulators?

The epigenome is at the interface between environmental factors and the genome, regulating gene transcription, DNA repair, and replication. Epigenetic modifications play a crucial role in establishing and maintaining cell identity and are especially crucial for neurology, musculoskeletal integrity, and the function of the immune system. Mutations in genes encoding for the components of the epigenetic machinery lead to the development of distinct disorders, especially involving the central nervous system and host defense. In this review, we focus on the role of epigenetic modifications for the function of the immune system. By studying the immune phenotype of patients with monogenic mutations in components of the epigenetic machinery (inborn errors of epigenetic regulators), we demonstrate the importance of DNA methylation, histone modifications, chromatin remodeling, noncoding RNAs, and mRNA processing for immunity. Moreover, we give a short overview on therapeutic strategies targeting the epigenome.

Alternative splicing: Human disease and quantitative analysis from high-throughput sequencing

Alternative splicing contributes to the majority of protein diversity in higher eukaryotes by allowing one gene to generate multiple distinct protein isoforms. It adds another regulation layer of gene expression. Up to 95% of human multi-exon genes undergo alternative splicing to encode proteins with different functions. Moreover, around 15% of human hereditary diseases and cancers are associated with alternative splicing. Regulation of alternative splicing is attributed to a set of delicate machineries interacting with each other in aid of important biological processes such as cell development and differentiation. Given the importance of alternative splicing events, their accurate mapping and quantification are paramount for downstream analysis, especially for associating disease with alternative splicing. However, deriving accurate isoform expression from high-throughput RNA-seq data remains a challenging task. In this mini-review, we aim to illustrate I) mechanisms and regulation of alternative splicing, II) alternative splicing associated human disease, III) computational tools for the quantification of isoforms and alternative splicing from RNA-seq.

HLA-G Expressing Immune Cells in Immune Mediated Diseases

HLA-G is a HLA class Ib antigen that possesses immunomodulatory properties. HLA-G-expressing CD4+ and CD8+ T lymphocytes, NK cells, monocytes, and dendritic cells with immunoregulatory functions are present in small percentages of patients with physiologic conditions. Quantitative and qualitative derangements of HLA-G+ immune cells have been detected in several conditions in which the immune system plays an important role, such as infectious, neoplastic, and autoimmune diseases as well as in complications from transplants and pregnancy. These observations strongly support the hypothesis that HLA-G+ immune cells may be implicated in the complex mechanisms underlying the pathogenesis of these disorders.

Identification of novel, clinically correlated autoantigens in the monogenic autoimmune syndrome APS1 by proteome-wide PhIP-Seq

The identification of autoantigens remains a critical challenge for understanding and treating autoimmune diseases. Autoimmune polyendocrine syndrome type 1 (APS1), a rare monogenic form of autoimmunity, presents as widespread autoimmunity with T and B cell responses to multiple organs. Importantly, autoantibody discovery in APS1 can illuminate fundamental disease pathogenesis, and many of the antigens found in APS1 extend to more common autoimmune diseases. Here, we performed proteome-wide programmable phage-display (PhIP-Seq) on sera from a cohort of people with APS1 and discovered multiple common antibody targets. These novel APS1 autoantigens exhibit tissue-restricted expression, including expression in enteroendocrine cells, pineal gland, and dental enamel. Using detailed clinical phenotyping, we find novel associations between autoantibodies and organ-restricted autoimmunity, including a link between anti-KHDC3L autoantibodies and premature ovarian insufficiency, and between anti-RFX6 autoantibodies and diarrheal-type intestinal dysfunction. Our study highlights the utility of PhIP-Seq for extensively interrogating antigenic repertoires in human autoimmunity and the importance of antigen discovery for improved understanding of disease mechanisms.

Clinical and Immunological Phenotype of Patients With Primary Immunodeficiency Due to Damaging Mutations in NFKB2

Non-canonical NF-κB-pathway signaling is integral in immunoregulation. Heterozygous mutations in NFKB2 have recently been established as a molecular cause of common variable immunodeficiency (CVID) and DAVID-syndrome, a rare condition combining deficiency of anterior pituitary hormone with CVID. Here, we investigate 15 previously unreported patients with primary immunodeficiency (PID) from eleven unrelated families with heterozygous NFKB2-mutations including eight patients with the common p.Arg853^* nonsense mutation and five patients harboring unique novel C-terminal truncating mutations. In addition, we describe the clinical phenotype of two patients with proximal truncating mutations. Cohort analysis extended to all 35 previously published NFKB2-cases revealed occurrence of early-onset PID in 46/50 patients (mean age of onset 5.9 years, median 4.0 years). ACTH-deficiency occurred in 44%. Three mutation carriers have deceased, four developed malignancies. Only two mutation carriers were clinically asymptomatic. In contrast to typical CVID, most patients suffered from early-onset and severe disease manifestations, including clinical signs of T cell dysfunction e.g., chronic-viral or opportunistic infections. In addition, 80% of patients suffered from (predominately T cell mediated) autoimmune (AI) phenomena (alopecia > various lymphocytic organ-infiltration > diarrhea > arthritis > AI-cytopenia). Unlike in other forms of CVID, auto-antibodies or lymphoproliferation were not common hallmarks of disease. Immunophenotyping showed largely normal or even increased quantities of naïve and memory CD4⁺ or CD8⁺ T-cells and normal T-cell proliferation. NK-cell number and function were also normal. In contrast, impaired B-cell differentiation and hypogammaglobinemia were consistent features of NFKB2-associated disease. In addition, an array of lymphocyte subpopulations, such as regulatory T cell, Th17-, cTFH-, NKT-, and MAIT-cell numbers were decreased. We conclude that heterozygous damaging mutations in NFKB2 represent a distinct PID entity exceeding the usual clinical spectrum of CVID. Impairment of the non-canonical NF-κB pathways affects function and differentiation of numerous lymphocyte-subpopulations and thus causes a heterogeneous, more severe form of PID phenotype with early-onset. Further characteristic features are multifaceted, primarily T cell-mediated autoimmunity, such as alopecia, lymphocytic organ infiltration, and in addition frequently ACTH-deficiency.

Primary immunodeficiency and autoimmunity: A comprehensive review

The primary immunodeficiency diseases (PIDs) include many genetic disorders that affect different components of the innate and adaptive responses. The number of distinct genetic PIDs has increased exponentially with improved methods of detection and advanced laboratory methodology. Patients with PIDs have an increased susceptibility to infectious diseases and non-infectious complications including allergies, malignancies and autoimmune diseases (ADs), the latter being the first manifestation of PIDs in several cases. There are two types of PIDS. Monogenic immunodeficiencies due to mutations in genes involved in immunological tolerance that increase the predisposition to develop autoimmunity including polyautoimmunity, and polygenic immunodeficiencies characterized by a heterogeneous clinical presentation that can be explained by a complex pathophysiology and which may have a multifactorial etiology. The high prevalence of ADs in PIDs demonstrates the intricate relationships between the mechanisms of these two conditions. Defects in central and peripheral tolerance, including mutations in AIRE and T regulatory cells respectively, are thought to be crucial in the development of ADs in these patients. In fact, pathology that leads to PID often also impacts the Treg/Th17 balance that may ease the appearance of a proinflammatory environment, increasing the odds for the development of autoimmunity. Furthermore, the influence of chronic and recurrent infections through molecular mimicry, bystander activation and super antigens activation are supposed to be pivotal for the development of autoimmunity. These multiple mechanisms are associated with diverse clinical subphenotypes that hinders an accurate diagnosis in clinical settings, and in some cases, may delay the selection of suitable pharmacological therapies. Herein, a comprehensively appraisal of the common mechanisms among these conditions, together with clinical pearls for treatment and diagnosis is presented.

Will the real Moebius syndrome please stand up? A systematic review of the literature and statistical cluster analysis of clinical features

Moebius syndrome is a highly variable syndrome with abducens and facial nerve palsy as core features. Strict diagnostic criteria do not exist and the inconsistency of the associated features makes determination difficult. To determine what features are associated with Moebius syndrome we performed a systematic literature review resulting in a composite case series of 449 individuals labeled with Moebius syndrome. We applied minimum criteria (facial and abducens palsy) to determine the prevalence of associated clinical features in this series. Additionally, we performed statistical cluster analysis to determine which features tended to occur together. Our study comprises the largest series of patients with Moebius syndrome and the first to apply statistical methodology to elucidate clinical relationships. We present evidence for two groups within the Moebius diagnosis. Type 1: exhibiting micrognathia, limb anomalies and feeding/swallowing difficulty that tend to occur together. Type 2: phenotypically diverse but more associated with radiologically detectable neurologic abnormalities and developmental delay.

Causes and pathophysiology of hypoparathyroidism

Hypoparathyroidism, a disorder characterized by hypocalcemia ensuing from inadequate parathyroid hormone secretion, is a rather rare disorder caused by multiple etiologies. When not caused by inadvertent damage or removal of the parathyroids during neck surgery, it is usually genetically determined. Epidemiological figures of this disease are still scarce and mainly limited to countries where non-anonymous databases are available and to surgical case series. Both the surgical and non-surgical forms pose diagnostic challenges. For surgical hypoparathyroidism, transient forms have to be ruled out even in the long term, in order to avoid unnecessary chronic replacement therapy with calcium and calcitriol. Regarding non-surgical hypoparathyroidism, once referred to as idiopathic, a systematic clinically and genetically-driven approach to define the precise diagnosis have to be pursued. In the case of syndromic hypoparathyroidism, patients have to be screened for associated abnormalities. Autoimmune, non-genetic hypoparathyroidism is still a diagnosis of exclusion, since no specific autoantibodies are specific for this condition.

Monogenic polyautoimmunity in primary immunodeficiency diseases

Primary immunodeficiency diseases (PIDs) consist of a large group of genetic disorders that affect distinct components of the immune system. PID patients are susceptible to infection and non-infectious complications, particularly autoimmunity. A specific group of monogenic PIDs are due to mutations in genes that are critical for the regulation of immunological tolerance and immune responses. This group of monogenic PIDs is at high risk of developing polyautoimmunity (i.e., the presence of more than one autoimmune disease in a single patient) because of their impaired immunity. In this review, we discuss the mechanisms of autoimmunity in PIDs and the characteristics of polyautoimmunity in the following PIDs: IPEX; monogenic IPEX-like syndrome; LRBA deficiency; CTLA4 deficiency; APECED; ALPS; and PKCδ deficiency.