Competing functions encoded in the allergy-associated F(c)epsilonRIbeta gene

Architecture of the high-affinity immunoglobulin E receptor

The high-affinity immunoglobulin E (IgE) receptor (FcεRI) drives type I hypersensitivity in response to allergen-specific IgE. FcεRI is a multimeric complex typically composed of one α, one β, and two disulfide-linked γ subunits. The α subunit binds to the fragment crystallizable (Fc) region of IgE (Fcε), whereas the β and γ subunits mediate signaling through their intracellular immunoreceptor tyrosine-based activation motifs (ITAMs). Here, we report cryo-electron microscopy (cryo-EM) structures of the apo state of FcεRI and of FcεRI bound to Fcε. At the transmembrane domain (TMD), the α and γ subunits associate to form a tightly packed, three-helix bundle (αγ2 bundle) with pseudo-threefold symmetry through extensive hydrophobic and polar interactions. The αγ2 bundle further assembles with the β subunit to complete the TMD, from which multiple ITAMs might extend into the cytoplasm for downstream signaling. The apo mouse FcεRI essentially forms an identical structure to that of the Fcε-bound sensitized form, suggesting that the binding of Fcε to FcεRI does not alter the overall conformation of the receptor. Furthermore, the juxtamembrane interaction between the extracellular domains (ECDs) of mouse FcεRIα and FcεRIβ is not observed between their human counterparts, which implies potential species-specific differences in receptor stability and activation. Our findings provide a framework for understanding the general structural principles underlying Fc receptor assembly, the signaling mechanism underlying type I hypersensitivity, and the design of efficient antiallergic therapeutics.

Regulation of Trafficking and Signaling of the High Affinity IgE Receptor by FcεRIβ and the Potential Impact of FcεRIβ Splicing in Allergic Inflammation

Mast cells are tissue-resident immune cells that function in both innate and adaptive immunity through the release of both preformed granule-stored mediators, and newly generated proinflammatory mediators that contribute to the generation of both the early and late phases of the allergic inflammatory response. Although mast cells can be activated by a vast array of mediators to contribute to homeostasis and pathophysiology in diverse settings and contexts, in this review, we will focus on the canonical setting of IgE-mediated activation and allergic inflammation. IgE-dependent activation of mast cells occurs through the high affinity IgE receptor, FcεRI, which is a multimeric receptor complex that, once crosslinked by antigen, triggers a cascade of signaling to generate a robust response in mast cells. Here, we discuss FcεRI structure and function, and describe established and emerging roles of the β subunit of FcεRI (FcεRIβ) in regulating mast cell function and FcεRI trafficking and signaling. We discuss current approaches to target IgE and FcεRI signaling and emerging approaches that could target FcεRIβ specifically. We examine how alternative splicing of FcεRIβ alters protein function and how manipulation of splicing could be employed as a therapeutic approach. Targeting FcεRI directly and/or IgE binding to FcεRI are promising approaches to therapeutics for allergic inflammation. The characteristic role of FcεRIβ in both trafficking and signaling of the FcεRI receptor complex, the specificity to IgE-mediated activation pathways, and the preferential expression in mast cells and basophils, makes FcεRIβ an excellent, but challenging, candidate for therapeutic strategies in allergy and asthma, if targeting can be realized.

Fc Receptor Variants and Disease: A Crucial Factor to Consider in the Antibody Therapeutics in Clinic

The fragment crystallizable (Fc) domain of antibodies is responsible for their protective function and long-lasting serum half-life via Fc-mediated effector function, transcytosis, and recycling through its interaction with Fc receptors (FcRs) expressed on various immune leukocytes, epithelial, and endothelial cells. Therefore, the Fc-FcRs interaction is a control point of both endogenous and therapeutic antibody function. There are a number of reported genetic variants of FcRs, which include polymorphisms in (i) extracellular domain of FcRs, which change their affinities to Fc domain of antibodies; (ii) both cytoplasmic and intracellular domain, which alters the extent of signal transduction; and (iii) the promoter region of the FcRs gene, which affects the expression level of FcRs, thus being associated with the pathogenesis of disease indications. In this review, we firstly describe the correlation between the genetic variants of FcRs and immunological disorders by individual differences in the extent of FcRs-mediated regulations. Secondly, we discuss the influence of the genetic variants of FcRs on the susceptibility to infectious diseases or cancer in the perspective of FcRs-induced effector functions. Overall, we concluded that the genetic variants of FcRs are one of the key elements in the design of antibody therapeutics due to their variety of clinical outcomes among individuals.

MetaCell: analysis of single-cell RNA-seq data using K-nn graph partitions

scRNA-seq profiles each represent a highly partial sample of mRNA molecules from a unique cell that can never be resampled, and robust analysis must separate the sampling effect from biological variance. We describe a methodology for partitioning scRNA-seq datasets into metacells: disjoint and homogenous groups of profiles that could have been resampled from the same cell. Unlike clustering analysis, our algorithm specializes at obtaining granular as opposed to maximal groups. We show how to use metacells as building blocks for complex quantitative transcriptional maps while avoiding data smoothing. Our algorithms are implemented in the MetaCell R/C++ software package.

PRMT1 Deficiency in Mouse Juvenile Heart Induces Dilated Cardiomyopathy and Reveals Cryptic Alternative Splicing Products

Protein arginine methyltransferase 1 (PRMT1) catalyzes the asymmetric dimethylation of arginine residues in proteins and methylation of various RNA-binding proteins and is associated with alternative splicing in vitro. Although PRMT1 has essential in vivo roles in embryonic development, CNS development, and skeletal muscle regeneration, the functional importance of PRMT1 in the heart remains to be elucidated. Here, we report that juvenile cardiomyocyte-specific PRMT1-deficient mice develop severe dilated cardiomyopathy and exhibit aberrant cardiac alternative splicing. Furthermore, we identified previously undefined cardiac alternative splicing isoforms of four genes (Asb2, Fbxo40, Nrap, and Eif4a2) in PRMT1-cKO mice and revealed that eIF4A2 protein isoforms translated from alternatively spliced mRNA were differentially ubiquitinated and degraded by the ubiquitin-proteasome system. These findings highlight the essential roles of PRMT1 in cardiac homeostasis and alternative splicing regulation.

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PRMT1 deficiency in cardiomyocytes causes dilated cardiomyopathy in juvenile mice

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PRMT1-deficient heart shows abnormal alternative splicing patterns

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Previously undefined cardiac splicing events are revealed by transcriptome analysis

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eIF4A2 isoforms are differentially ubiquitinated and degraded

An Overview of Recent Advances and Clinical Applications of Exon Skipping and Splice Modulation for Muscular Dystrophy and Various Genetic Diseases

Exon skipping is a therapeutic approach that is feasible for various genetic diseases and has been studied and developed for over two decades. This approach uses antisense oligonucleotides (AON) to modify the splicing of pre-mRNA to correct the mutation responsible for a disease, or to suppress a particular gene expression, as in allergic diseases. Antisense-mediated exon skipping is most extensively studied in Duchenne muscular dystrophy (DMD) and has developed from in vitro proof-of-concept studies to clinical trials targeting various single exons such as exon 45 (casimersen), exon 53 (NS-065/NCNP-01, golodirsen), and exon 51 (eteplirsen). Eteplirsen (brand name Exondys 51), is the first approved antisense therapy for DMD in the USA, and provides a treatment option for ~14% of all DMD patients, who are amenable to exon 51 skipping. Eteplirsen is granted accelerated approval and marketing authorization by the US Food and Drug Administration (FDA), on the condition that additional postapproval trials show clinical benefit. Permanent exon skipping achieved at the DNA level using clustered regularly interspaced short palindromic repeats (CRISPR) technology holds promise in current preclinical trials for DMD. In hopes of achieving clinical success parallel to DMD, exon skipping and splice modulation are also being studied in other muscular dystrophies, such as Fukuyama congenital muscular dystrophy (FCMD), dysferlinopathy including limb-girdle muscular dystrophy type 2B (LGMD2B), Miyoshi myopathy (MM), and distal anterior compartment myopathy (DMAT), myotonic dystrophy, and merosin-deficient congenital muscular dystrophy type 1A (MDC1A). This chapter also summarizes the development of antisense-mediated exon skipping therapy in diseases such as Usher syndrome, dystrophic epidermolysis bullosa, fibrodysplasia ossificans progressiva (FOP), and allergic diseases.

Mast cells in asthma--state of the art

Mast cells (MCs) play a central role in tissue homoeostasis, sensing the local environment through numerous innate cell surface receptors. This enables them to respond rapidly to perceived tissue insults with a view to initiating a co-ordinated programme of inflammation and repair. However, when the tissue insult is chronic, the ongoing release of multiple pro-inflammatory mediators, proteases, cytokines and chemokines leads to tissue damage and remodelling. In asthma, there is strong evidence of ongoing MC activation, and their mediators and cell-cell signals are capable of regulating many facets of asthma pathophysiology. This article reviews the evidence behind this.

Mast cells in airway diseases and interstitial lung disease

Mast cells are major effector cells of inflammation and there is strong evidence that mast cells play a significant role in asthma pathophysiology. There is also a growing body of evidence that mast cells contribute to other inflammatory and fibrotic lung diseases such as chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis. This review discusses the role that mast cells play in airway diseases and highlights how mast cell microlocalisation within specific lung compartments and their cellular interactions are likely to be critical for their effector function in disease.

The MS4A family: counting past 1, 2 and 3

The MS4A (membrane-spanning 4-domain family, subfamily A) family of proteins contains some well-known members including MS4A1 (CD20), MS4A2 (FcɛRIβ) and MS4A3 (HTm4). These three MS4A family members are expressed on the cell surface of specific leukocyte subsets and have been well characterized as having key roles in regulating cell activation, growth and development. However, beyond MS4A1-3 there are a large number of related molecules (18 to date in humans) where our understanding of their biological roles is at a relatively nascent stage. This review examines the larger MS4A family focusing on their structure, expression, regulation and characterized and/or emerging biological roles. Our own work on one family member MS4A8B, and its possible role in epithelial cell regulation, is also highlighted.

Fine-Tuning of Mast Cell Activation by FcεRIβ Chain

Mast cells play a key role in allergic reaction and disorders through the high affinity receptor for IgE (Fc_εRI) which is primarily activated by IgE and antigen complex. In humans, mast cells express two types of Fc_εRI on the cell surface, tetrameric αβγ₂ and trimeric αγ₂, whereas in mice, the tetrameric αβγ₂ type is exclusively expressed. In human allergic inflammation lesions, mast cells increase in number and preferentially express the αβγ₂ type Fc_εRI. By contrast, in the lesion of non-allergic inflammation, mast cells mainly express the αγ₂type. Since the β chain amplifies the expression and signaling of FcεRI, mast cell effector functions and allergic reaction in vivo are enhanced in the presence of the β chain. In contrast, a truncated β chain-isoform (βT) inhibits FcεRI surface expression. The human Fc_εRIβ gene contains seven exons and a repressor element located in the forth intron, through which Fc_εRIβ transcription is repressed in the presence of GM-CSF. Regarding the additional signal regulatory function of the β chain, the β chain ITAM has dual (positive and negative) functions in the regulation of the mast cell activation. Namely, the Fc_εRIβ chain ITAM enhances the mast cell activation signal triggered by a low-intensity (weak) stimulation whereas it suppresses the signal triggered by high-intensity (strong) stimulation. In an oxazolone-induced mouse CHS model, IgE-mediated mast cell activation is required and the β chain ITAM is crucially involved. Adenosine receptor, one of the GPCRs, triggers a synergistic degranulation response with FcεRI in mast cells, for which the β chain ITAM critically plays positive role, possibly reflecting the in vivo allergic response. These regulatory functions of the FcεRIβ ITAM finely tune FcεRI-induced mast cell activation depending on the stimulation strength, enabling the Fc_εRIβ chain to become a potential molecular target for the development of new strategies for therapeutic interventions for allergies.

The high affinity IgE receptor (FcεRI) expression and function in airway smooth muscle

The airway smooth muscle (ASM) is no longer considered as merely a contractile apparatus and passive recipient of growth factors, neurotransmitters and inflammatory mediators signal but a critical player in the perpetuation and modulation of airway inflammation and remodeling. In recent years, a molecular link between ASM and IgE has been established through Fc epsilon receptors (FcεRs) in modulating the phenotype and function of these cells. Particularly, the expression of high affinity IgE receptor (FcεRI) has been noted in primary human ASM cells in vitro and in vivo within bronchial biopsies of allergic asthmatic subjects. The activation of FcεRI on ASM cells suggests a critical yet almost completely ignored network which may modulate ASM cell function in allergic asthma. This review is intended to provide a historical perspective of IgE effects on ASM and highlights the recent updates in the expression and function of FcεRI, and to present future perspectives of activation of this pathway in ASM cells.

Expression proteomics of UPF1 knockdown in HeLa cells reveals autoregulation of hnRNP A2/B1 mediated by alternative splicing resulting in nonsense-mediated mRNA decay

Background

In addition to acting as an RNA quality control pathway, nonsense-mediated mRNA decay (NMD) plays roles in regulating normal gene expression. In particular, the extent to which alternative splicing is coupled to NMD and the roles of NMD in regulating uORF containing transcripts have been a matter of debate.

Results

In order to achieve a greater understanding of NMD regulated gene expression we used 2D-DiGE proteomics technology to examine the changes in protein expression induced in HeLa cells by UPF1 knockdown. QPCR based validation of the corresponding mRNAs, in response to both UPF1 knockdown and cycloheximide treatment, identified 17 bona fide NMD targets. Most of these were associated with bioinformatically predicted NMD activating features, predominantly upstream open reading frames (uORFs). Strikingly, however, the majority of transcripts up-regulated by UPF1 knockdown were either insensitive to, or even down-regulated by, cycloheximide treatment. Furthermore, the mRNA abundance of several down-regulated proteins failed to change upon UPF1 knockdown, indicating that UPF1's role in regulating mRNA and protein abundance is more complex than previously appreciated. Among the bona fide NMD targets, we identified a highly conserved AS-NMD event within the 3' UTR of the HNRNPA2B1 gene. Overexpression of GFP tagged hnRNP A2 resulted in a decrease in endogenous hnRNP A2 and B1 mRNA with a concurrent increase in the NMD sensitive isoforms.

Conclusions

Despite the large number of changes in protein expression upon UPF1 knockdown, a relatively small fraction of them can be directly attributed to the action of NMD on the corresponding mRNA. From amongst these we have identified a conserved AS-NMD event within HNRNPA2B1 that appears to mediate autoregulation of HNRNPA2B1 expression levels.

A novel FcεRIβ-chain truncation regulates human mast cell proliferation and survival

Mast cells contribute to allergy through IgE-dependent activation via the high-affinity IgE receptor FcεRI. The role of the FcεRIβ chain (MS4A2) in mast cell function is not understood fully, although it serves to amplify FcεRI-dependent signaling. We demonstrate the expression of a novel MS4A2 truncation lacking exon 3 in human mast cells termed MS4A2(trunc). MS4A2(trunc) gene expression was regulated negatively by the mast cell growth factor stem cell factor (SCF), and its expression was not detected in the SCF receptor gain-of-function human mast cell line HMC-1. Unlike MS4A2, MS4A2(trunc) did not traffic to the cytoplasmic membrane but instead was associated with the nuclear membrane. Overexpression of MS4A2(trunc) induced human lung mast cell death and profoundly inhibited HMC-1 cell proliferation by inducing G(2)-phase cell cycle arrest and apoptosis. Thus, we have identified a novel splice variant of MS4A2 that might be important in the regulation of human mast cell proliferation and survival. This finding demonstrates that the MS4A2 gene has multiple roles, extending beyond the regulation of acute allergic responses. By understanding the mechanisms regulating its function, it might be possible to induce its expression in mast cells in vivo, which could lead to better treatments for diseases such as mastocytosis and asthma.

The signal peptide of the IgE receptor alpha-chain prevents surface expression of an immunoreceptor tyrosine-based activation motif-free receptor pool

The high affinity receptor for IgE, Fc epsilon receptor I (FcepsilonRI), is an activating immune receptor and key regulator of allergy. Antigen-mediated cross-linking of IgE-loaded FcepsilonRI alpha-chains induces cell activation via immunoreceptor tyrosine-based activation motifs in associated signaling subunits, such as FcepsilonRI gamma-chains. Here we show that the human FcepsilonRI alpha-chain can efficiently reach the cell surface by itself as an IgE-binding receptor in the absence of associated signaling subunits when the endogenous signal peptide is swapped for that of murine major histocompatibility complex class-I H2-K(b). This single-chain isoform of FcepsilonRI exited the endoplasmic reticulum (ER), trafficked to the Golgi and, subsequently, trafficked to the cell surface. Mutational analysis showed that the signal peptide regulates surface expression in concert with other described ER retention signals of FcepsilonRI-alpha. Once the FcepsilonRI alpha-chain reached the cell surface by itself, it formed a ligand-binding receptor that stabilized upon IgE contact. Independently of the FcepsilonRI gamma-chain, this single-chain FcepsilonRI was internalized after receptor cross-linking and trafficked into a LAMP-1-positive lysosomal compartment like multimeric FcepsilonRI. These data suggest that the single-chain isoform is capable of shuttling IgE-antigen complexes into antigen loading compartments, which plays an important physiologic role in the initiation of immune responses toward allergens. We propose that, in addition to cytosolic and transmembrane ER retention signals, the FcepsilonRI alpha-chain signal peptide contains a negative regulatory signal that prevents expression of an immunoreceptor tyrosine-based activation motif-free IgE receptor pool, which would fail to induce cell activation.

Functional and clinical consequences of Fc receptor polymorphic and copy number variants

Receptors for immunoglobulins (Fc receptors) play a central role during an immune response, as they mediate the specific recognition of antigens of almost infinite diversity by leucocytes, thereby linking the humoral and cellular components of immunity. Indeed, engagement of Fc receptors by immunoglobulins initiates a range of immunoregulatory processes that might also play a role in disease pathogenesis. In the circulation, five main types of immunoglobulins (Ig) exist - namely IgG, IgA, IgE, IgM and IgD and receptors with the ability to recognize and bind to IgG (Fc gamma receptor family), IgE (Fc epsilon RI and CD23), IgA (CD89; Fc alpha/microR) and IgM (Fc alpha/microR) have been identified and characterized. However, it is astonishing that nearly all the known human Fc receptors display extensive genetic variation with clear implications for their function, thus representing a substantial genetic risk factor for the pathogenesis of a range of chronic inflammatory disorders.

IgE signaling suppresses FcepsilonRIbeta expression

Activation of the high-affinity receptor for IgE, FcepsilonRI, is known to elicit its rapid down-regulation through internalization and degradation. In keeping with this, expression of all three FcepsilonRI subunits is decreased at the protein level after cross-linkage of IgE with antigen. However, we find that the FcepsilonRI beta-subunit is also selectively suppressed at the mRNA level, through a pathway primarily involving Fyn, Syk, PI3K, and NF-kappaB. IgG or calcium ionophore, stimuli known to mimic portions of the IgE signaling cascade, similarly suppressed beta-subunit expression. LPS, a NF-kappaB-activating TLR ligand, did not alter beta-subunit expression. As IgE increases FcepsilonRI expression, we examined the coordinated regulation of FcepsilonRI subunits during culture with IgE, followed by cross-linkage with antigen. IgE increased the expression of all three FcepsilonRI subunits and strikingly induced expression of the antagonistic beta(T). The ratio of beta:beta(T) protein expression decreased significantly during culture with IgE and was reset to starting levels by antigen cross-linkage. These changes in protein levels were matched by similar fluctuations in beta and beta(T) mRNAs. FcepsilonRIbeta is a key regulator of IgER expression and function, a gene in which polymorphisms correlate with allergic disease prevalence. The ability of IgE and FcepsilonRI signaling to coordinate expression of the beta and beta(T) subunits may comprise a homeostatic feedback loop-one that could promote chronic inflammation and allergic disease if dysregulated.

High-affinity IgE receptor-beta chain expression in human mast cells

The high-affinity IgE receptor (FcεRI)-β gene is one of the atopy-associated genes, but its biological significance is largely unknown. In this study, we generated the anti-FcεRI-β chain antibody to clarify β-chain protein expression in human mast cells. The FcεRI-β antibody showed specific binding to a 27 kDa protein with Western blotting and membrane bound immunostaining using cultured mast cells. Monomeric IgE sensitization increased β-chain expression as well as mature α-chain expression in mast cells. Upregulation of β-chain expression with monomeric IgE treatment suggests possible roles of FcεRI-β protein as an atopy-related molecule.

Discovering susceptibility genes for asthma and allergy

Asthma and asthma-related traits are complex diseases with strong genetic and environmental components. Rapid progress in asthma genetics has led to the identification of several candidate genes that are associated with asthma-related traits. Typically the phenotypic impact of each of these genes, including the ones most often replicated in association studies, is mild, but larger effects may occur when multiple variants synergize within a permissive environmental context. Despite the achievements made in asthma genetics formidable challenges remain. The development of novel, powerful tools for gene discovery, and a closer integration of genetics and biology, should help to overcome these challenges.

NMD: multitasking between mRNA surveillance and modulation of gene expression

Gene expression is a highly specific and regulated multilayer process with a plethora of interconnections as well as safeguard and feedback mechanisms. Messenger RNA, long neglected as a mere subcarrier of genetic information, is more recently recognized as a linchpin of regulation and control of gene expression. Moreover, the awareness of not only proteins but also mRNA as a modulator of genetic disorders has vastly increased in recent years. Nonsense-mediated mRNA decay (NMD) is a posttranscriptional surveillance mechanism that uses an intricate network of nuclear and cytoplasmic processes to eliminate mRNAs, containing premature termination codons. It thus helps limit the synthesis of potentially harmful truncated proteins. However, recent results suggest functions of NMD that go far beyond this role and affect the expression of wild-type genes and the modulation of whole pathways. In both respects--the elimination of faulty transcripts and the regulation of error-free mRNAs--NMD has many medical implications. Therefore, it has earned increasing interest from researchers of all fields of the life sciences. In the following text, we (1) present current knowledge about the NMD mechanism and its targets, (2) define its relevance in the regulation of important biochemical pathways, (3) explore its medical significance and the prospects of therapeutic interventions, and (4) discuss additional functions of NMD effectors, some of which may be networked to NMD. The main focus of this chapter lies on mammalian NMD and resorts to the features and factors of NMD in other organisms if these help to complete or illuminate the picture.

Decoding IgE Fc receptors

Immunoglobulin E (IgE) plays a central role in the pathogenesis of allergic diseases by interacting with two membrane receptors: high-affinity FcepsilonRI and low-affinity FcepsilonRII (CD23). Allergeninduced IgE-occupied FcepsilonRI aggregation on the mast cell or basophil cell surface leads to the activation of intracellular signaling events and eventually the release of pre-formed and de novo synthesized inflammatory mediators. The role of FcepsilonRII in allergic diseases has been proposed to include regulation of IgE synthesis, enhanced histamine release from basophils, and a contribution to Ag-IgE complex presentation but the exact function of CD23 remains poorly understood. This review summarizes some new developments in IgE Fc-receptor studies with an emphasis on regulation of FcepsilonRI expression and signal transduction, including monomeric IgE, lipid raft segregation, and some recently identified negative regulators. A better understanding of signaling events following IgE FcR aggregation will shed new light on how allergy patients might be treated more safely and effectively.

Regulation of the mast cell response to the type 1 Fc epsilon receptor

The type I Fc epsilon receptor (Fc epsilon RI) is one of the better understood members of its class and is central to the immunological activation of mast cells and basophils, the key players in immunoglobulin E (IgE)-dependent immediate hypersensitivity. This review provides background information on several distinct regulatory mechanisms controlling this receptor's stimulus-response coupling network. First, we review the current understanding of this network's operation, and then we focus on the inhibitory regulatory mechanisms. In particular, we discuss the different known cytosolic molecules (e.g. kinases, phosphatases, and adapters) as well as cell membrane proteins involved in negatively regulating the Fc epsilon RI-induced secretory responses. Knowledge of this field is developing at a fast rate, as new proteins endowed with regulatory functions are still being discovered. Our understanding of the complex networks by which these proteins exert regulation is limited. Although the scope of this review does not include addressing several important biochemical and biophysical aspects of the regulatory mechanisms, it does provide general insights into a central field in immunology.

New developments in FcepsilonRI regulation, function and inhibition

The high-affinity Fc receptor for IgE (FcepsilonRI), a multimeric immune receptor, is a crucial structure for IgE-mediated allergic reactions. In recent years, advances have been made in several important areas of the study of FcepsilonRI. The first area relates to FcepsilonRI-mediated biological responses that are antigen independent. The second area encompasses the biological relevance of the distinct signalling pathways that are activated by FcepsilonRI; and the third area relates to the accumulated evidence for the tight control of FcepsilonRI signalling through a broad array of inhibitory mechanisms, which are being developed into promising therapeutic approaches.

Histamine release from the basophils of control and asthmatic subjects and a comparison of gene expression between "releaser" and "nonreleaser" basophils

Most human blood basophils respond to FcepsilonRI cross-linking by releasing histamine and other inflammatory mediators. Basophils that do not degranulate after anti-IgE challenge, known as "nonreleaser" basophils, characteristically have no or barely detectable levels of the Syk tyrosine kinase. The true incidence of the nonreleaser phenotype, its relationship (if any) to allergic asthma, and its molecular mechanism are not well understood. In this study, we report statistical analyses of degranulation assays performed in 68 control and 61 asthmatic subjects that establish higher basal and anti-IgE-stimulated basophil degranulation among the asthmatics. Remarkably, 28% of the control group and 13% of the asthmatic group were nonreleasers for all or part of our 4-year long study and cycling between the releaser and nonreleaser phenotypes occurred at least once in blood basophils from 8 (of 8) asthmatic and 16 (of 23) control donors. Microarray analysis showed that basal gene expression was generally lower in nonreleaser than releaser basophils. In releaser cells, FcepsilonRI cross-linking up-regulated >200 genes, including genes encoding receptors (the FcepsilonRI alpha and beta subunits, the histamine 4 receptor, the chemokine (C-C motif) receptor 1), signaling proteins (Lyn), chemokines (IL-8, RANTES, MIP-1alpha, and MIP-1beta) and transcription factors (early growth response-1, early growth response-3, and AP-1). FcepsilonRI cross-linking induced fewer, and quite distinct, transcriptional responses in nonreleaser cells. We conclude that "nonreleaser" and "cycler" basophils represent a distinct and reversible natural phenotype. Although histamine is more readily released from basophils isolated from asthmatics than controls, the presence of nonreleaser basophils does not rule out the diagnosis of asthma.

Exonization of Alu-generated splice variants in the survivin gene of human and non-human primates

Survivin is a member of the inhibitor apoptosis family that is overexpressed in many malignancies. It has five known alternative splice forms, some of which differ in their antiapoptotic properties and expression levels in human cancers. Here we describe a novel donor splice site (DSS), 2B+32 DSS, which is used in conjunction with survivin alternative exon 2B, resulting in the inclusion of 32 additional nucleotides from intron 2 at the 3' end of this exon. Sequence analysis showed that both the classical exon 2B DSS and 2B+32 are provided by an Alu sequence, which is inserted in intron 2 downstream of a functional acceptor splice site, leading to the exonization of part of the repetitive element. Minor transcripts including the 2B+32 alternative exon, or retaining the whole intronic region comprised between exons 2B and 3, were detected in several human cell lines and in some human tissues. Survivin 2B+32 containing variants acquire a premature stop codon (PTC) and may therefore be degraded by the nonsense mediated decay pathway. The implication of these novel isoforms, as well as other PTC+ survivin variants, in the overall regulation of survivin expression is discussed. Sequence analysis of intron 2 which contains the Alu Y element was performed on different primate species in order to trace its insertion and exonization during primate evolution.

Fcε- and Fcγ-receptor signaling in diseases

It has become increasingly clear that receptors for the immunoglobulin Fc region play pivotal roles in immune homeostasis and disease. This review describes the fine regulation of the high-affinity IgE-receptor (FcepsilonRI) signaling, especially focusing on the early events that are coordinately regulated by Src family protein tyrosine kinases (PTKs), FcepsilonRI beta-subunit, and membrane lipid rafts. Because allergen-mediated FcepsilonRI cross-linking leads to the synthesis and release of a variety of proinflammatory mediators and cytokines, the duration and amplitude of the signal need to be strictly controlled, and the counterbalancing signaling is provided by specialized inhibitory receptors and molecules. However, recent work have revealed that Src family PTKs and FcepsilonRI beta-subunit transduce both positive and negative signaling with unexpectedly complex mechanisms. FcgammaRIIB exerts a unique inhibitory function on cell activation processes after the engagement of Fcgamma, FcepsilonRI and B cell receptors. Recent work has shown that FcgammaRIIB polymorphisms are associated with systemic lupus erythematosus, and that a transmembrane polymorphism in FcgammaRIIB results in an impaired distribution to lipid rafts and a reduced inhibitory function. Studies addressing the functions of disease-associated polymorphisms in the FcepsilonRI beta-subunit and low-affinity FcgammaRs are also considered.

Molecular Mechanisms for Transcriptional Regulation of Human High-Affinity IgE Receptor β-Chain Gene Induced by GM-CSF

The beta-chain of the high-affinity receptor for IgE (FcepsilonRI) plays an important role in regulating activation of FcepsilonRI-expressing cells such as mast cells in allergic reactions. We already reported that the transcription factor myeloid zinc finger (MZF) 1 which formed a high m.w. complex including four and a half LIM-only protein (FHL)3 in the nucleus repressed human beta-chain gene expression through an element in the fourth intron. We also found that GM-CSF induced expression of MZF-1 and nuclear translocation of FHL3. We screened a human cDNA library and identified NFY which was reported to bind histone deacetylases (HDACs) as a constituent of the complex. The C-subunit of NFY was demonstrated to form a ternary complex with MZF-1/FHL3 and interact with a beta-chain gene region including the element in the fourth intron. HDAC1 and HDAC2 were also shown to interact with the fourth intron region of the beta-chain gene. In a human mast cell line HMC-1 cultured with GM-CSF, both beta-chain expression and acetylation of histones interacting with the fourth intron region of the beta-chain gene were decreased. Collectively, these results indicated that HDACs, which were recruited to the beta-chain gene through the element in the fourth intron by MZF-1/FHL3/NFY, repressed beta-chain gene transcription by deacetylation of histones in the presence of GM-CSF. These mechanisms will be involved in not only the cell type-specific repression of beta-chain gene expression in differentiating hemopoietic cells but also the repression of beta-chain gene expression in the peripheral cells under specific circumstances.

IgE and FcepsilonRI regulation

The high-affinity immunoglobulin (Ig)E receptor, FcepsilonRI, regulates the action of mast cells and basophils and therefore, regulates the expression of atopic disease. There have been several recent observations that demonstrate new behaviors for this receptor. The control of FcepsilonRI expression, control of cell function by FcepsilonRI, and expression of FcepsilonRI on other cell types are important new areas of understanding currently being explored.

The high-affinity IgE receptor (FcepsilonRI): a critical regulator of airway smooth muscle cells?

The airway smooth muscle (ASM) has been typically described as a contractile tissue, responding to neurotransmitters and inflammatory mediators. However, it has recently been recognized that ASM cells can also secrete cytokines and chemokines and express cell adhesion molecules that are important for the perpetuation and modulation of airway inflammation. Recent progress has revealed the importance of IgE Fc receptors in stimulating and modulating the function of these cells. In particular, the high-affinity receptor for IgE (FcepsilonRI) has been identified in primary human ASM cells in vitro and in vivo within bronchial biopsies of atopic asthmatic individuals. Moreover, activation of this receptor has been found to induce marked increases in the intracellular calcium concentrations and T helper 2 cytokines and chemokines release. This and other evidence discussed in this review provide an emerging view of FcepsilonR/IgE network as a critical modulator of ASM cell function in allergic asthma.

Are basophil histamine release and high affinity IgE receptor expression involved in asymptomatic skin sensitization?

BACKGROUND

Immunoglobulin (Ig)E-sensitized persons with positive skin prick test, but no allergy symptoms, are classified as being asymptomatic skin sensitized (AS). The allergic type 1 disease is dependant on IgE binding to the high affinity IgE-receptor (FcepsilonRI) expressed on basophils and mast cells. However, a relationship between the AS status and FcepsilonRI has not been investigated. We aimed to characterize basophils from AS by looking at histamine release (HR) (sensitivity and reactivity) and the FcepsilonRI molecule, and compare it with nonatopic (NA) or allergic (A) persons.

METHODS

Blood was obtained from NA (n = 14), grass and/or birch A persons (n = 17) and mono-sensitized grass or birch pollen AS (n = 12). The basophil sensitivity and reactivity were examined by anti-IgE triggered HR. Surface expression of FcepsilonRI and IgE were measured by flow cytometry, FcepsilonRIalpha protein was identified using a radioimmunoassay and Western blot. mRNA coding for the classic FcepsilonRIbeta-chain and the truncated form (FcepsilonRIbetaT) were determined by real-time PCR.

RESULTS

The AS group was less reactive than NA or A persons when triggered by anti-IgE and had a significant higher number of nonresponders. However, there was no difference in sensitivity among the three groups and furthermore; the groups did not vary in FcepsilonRI- and IgE-surface expression, FcepsilonRIalpha-protein level or beta/betaT ratio.

CONCLUSION

Basophils from AS persons are less reactive and include more nonresponders than basophils from NA and A persons, but do not differ regarding the FcepsilonRI molecule.

Transport of the IgE receptor alpha-chain is controlled by a multicomponent intracellular retention signal

The human high affinity IgE receptor (FcepsilonRI) is a central component of the allergic response and is expressed as either a trimeric alphagamma2 or tetrameric alphabetagamma2 complex. It has been previously described that the cytoplasmic domain (CD) of the alpha-chain carries a dilysine motif at positions -3/-7 from the C terminus that functions in intracellular retention prior to assembly with other FcepsilonRI subunits. In this report we have further explored the role of the -3/-7 dilysine signal in controlling steady-state alpha-chain transport by mutational analysis and found little surface expression of a -3/-7 dialanine alpha-chain mutant but significant Golgi localization. We compared the transport properties of a series of alpha-chain cytoplasmic domain truncation mutants and observed that truncation mutants lacking 23 or more C-terminal residues showed a dramatic increase in steady-state transport suggesting a role for the membrane-proximal CD sequence in alpha-chain retention. By performing alanine-scanning mutagenesis we identified a dilysine sequence (Lys(212)-Lys(216)) proximal to the transmembrane domain (TMD) that is important for both alpha-chain cell-surface expression and intracellular stability. Furthermore, co-mutation of the Lys(212)-Lys(216) residues with the -3/-7 dilysine signal produced a dramatic increase in alpha-chain surface expression that was further increased by co-mutation of the lone charged residue (Asp(192)) in the TMD thereby defining three regions that function to regulate alpha-chain transport and in a highly synergistic manner.

Fc receptors as determinants of allergic reactions

Activation of the high-affinity receptor for IgE (FcepsilonRI) on allergic effector cells induces a multitude of positive signals via immunoreceptor tyrosine-based activation motifs, which leads to the rapid manifestation of allergic inflammatory reactions. As a counterbalance, the coaggregation of the IgG receptor FcgammaRIIB mediates inhibitory signals via immunoreceptor tyrosine-based inhibition motifs. Advances in the positive and negative regulation of Fc receptor expression and signaling have shed light on the role of Fc receptors in our immune system, indicating them to be bifunctional, inhibitory and activating structures. Based on these findings, exciting new therapeutic strategies have been developed, such as the use of chimeric fusion proteins, which concomitantly activate FcepsilonRI and FcgammaRIIB. These new approaches successfully take advantage of the bivalent character of Fc receptors and pave the way for innovative strategies to modulate allergic immune reactions.

Negative Signaling in Fc Receptor Complexes

Cell activation results from the transient displacement of an active balance between positive and negative signaling. This displacement depends in part on the engagement of cell surface receptors by extracellular ligands. Among these are receptors for the Fc portion of immunoglobulins (FcRs). FcRs are widely expressed by cells of hematopoietic origin. When binding antibodies, FcRs provide these cells with immunoreceptors capable of triggering numerous biological responses in response to a specific antigen. FcR-dependent cell activation is regulated by negative signals which are generated together with positive signals within signalosomes that form upon FcR engagement. Many molecules involved in positive signaling, including the FcRbeta subunit, the src kinase lyn, the cytosolic adapter Grb2, and the transmembrane adapters LAT and NTAL, are indeed also involved in negative signaling. A major player in negative regulation of FcR signaling is the inositol 5-phosphatase SHIP1. Several layers of negative regulation operate sequentially as FcRs are engaged by extracellular ligands with an increasing valency. A background protein tyrosine phosphatase-dependent negative regulation maintains cells in a "resting" state. SHIP1-dependent negative regulation can be detected as soon as high-affinity FcRs are occupied by antibodies in the absence of antigen. It increases when activating FcRs are engaged by multivalent ligands and, further, when FcR aggregation increases, accounting for the bell-shaped dose-response curve observed in excess of ligand. Finally, F-actin skeleton-associated high-molecular weight SHIP1, recruited to phosphorylated ITIMs, concentrates in signaling complexes when activating FcRs are coengaged with inhibitory FcRs by immune complexes. Based on these data, activating and inhibitory FcRs could be used for new therapeutic approaches to immune disorders.

Regulation of allergy by Fc receptors

The aggregation of high-affinity IgE receptors (FcepsilonRI) on mast cells and basophils has long been known as the critical event that initiates allergic reactions. Monomeric IgE was recently found to induce a variety of effects when binding to FcepsilonRI. Upregulation of FcepsilonRI only requires binding, whereas other responses require FcepsilonRI aggregation. Interestingly, FcepsilonRI aggregation has recently been understood to generate a mixture of positive and negative intracellular signals. Mast cells and basophils also express low-affinity and, under specific conditions, high-affinity IgG receptors. When co-engaging these receptors with FcepsilonRI, IgG antibodies can amplify or dampen IgE-induced mast cell activation. On the basis of these findings, it has been proposed that FcRs can be used as targets and/or tools for new therapeutic approaches to allergies.

IgE and Fc{epsilon}RI regulation

A central feature of allergic reactions is the aggregation of the high-affinity IgE receptor, FcepsilonRI, to initiate a change in the behavior of the cell expressing the receptor. It is now clear that a number of cell types can express this receptor, which broadens the biology that revolves around IgE antibody. It is also quite clear that the presence of monomeric IgE antibody alters the expression of FcepsilonRI. There remains considerable uncertainty about the importance of independent regulation of the FcepsilonRIbeta subunit or its splice variant beta(T), in terms of regulating both expression and function of FcepsilonRI. There is also only primitive understanding of the role of various polymorphisms in the subunit genes on the atopic phenotype. There are, however, many efforts being made to resolve these issues and to discover other factors that regulate expression of this receptor. Of particular interest for understanding the variation in expression in atopy among patients, the role of this receptor on non-mast cell/basophils will be important to elucidate.

A comparative study of the FcepsilonRI molecule on human mast cell and basophil cell lines

BACKGROUND

Mast cells and basophils express the high-affinity IgE receptor FcepsilonRI. We have analysed the human mast cell line LAD2 and four subclones of the basophil cell line KU812 in order to reveal possible differences concerning the FcepsilonRI surface regulation, anti-IgE-triggered activation, FcepsilonRIalpha protein stability and the mRNA level of FcepsilonRIalpha-, beta- and the truncated beta-chain (beta(T)), and thereby determine the utility of these cell lines in investigations of the FcepsilonRI biology.

METHODS

The surface expression of FcepsilonRI was assessed by flow cytometry, using the monoclonal antibody CRA1. The FcepsilonRI-induced cellular activation (i.e. cross-linking of FcepsilonRI) was determined by changes in the intracellular level of Ca2+, which was measured by fluorescence of Fura-2. The level of the FcepsilonRIalpha protein was determined by a Western blot technique and by a radioimmunoassay. The mRNA level of FcepsilonRIalpha, beta- and beta(T)-chain was analysed using real-time PCR.

RESULTS

Two KU812 subclones and especially LAD2 had FcepsilonRI surface expression which was capable of inducing cellular activation. Both the FcepsilonRI expression and stability of the FcepsilonRIalpha protein were increased when IgE was present. All the cell lines expressed mRNA of FcepsilonRIalpha-, beta- and beta(T), with LAD2 tending to have the highest expression. However, a determination of the beta/beta(T) ratio demonstrated no difference between any of the cell clones.

CONCLUSION

These cell lines are important tools in the investigation of both the FcepsilonRI molecule and the effects induced by its activation.

Fc receptor targeting in the treatment of allergy, autoimmune diseases and cancer

Immune activation and inhibitory receptors play an important role in the maintenance of an adequate activation threshold of various cells in our immune system. Analyses of murine models show that the inhibitory Fcreceptor, FcgammaRIIB plays an indispensable role in the suppression of anti-body-mediated allergy and autoimmunity. In contrast, the activating-type Fcreceptors (FcRs) are essential for the development of these diseases, suggesting that regulation of inhibitory or activating FcR is an ideal target as a therapeutic agent. In addition, recent crystal structural analyses of FcR-Ig-Fc fragment complexes provide an effective approach for developing FcR-targeting drugs. This review summarises recent advances of FcR, which were mainly obtained by murine studies, and highlights novel antibodies as possible FcR-targeting therapies for allergy, autoimmune diseases and cancer.

Cotranslational endoplasmic reticulum assembly of FcepsilonRI controls the formation of functional IgE-binding receptors

The human high affinity receptor for IgE (FcepsilonRI) is a cell surface structure critical for the pathology of allergic reactions. Human FcepsilonRI is expressed as a tetramer (alphabetagamma(2)) on basophils or mast cells and as trimeric (alphagamma(2)) complex on antigen-presenting cells. Expression of the human alpha subunit can be down-regulated by a splice variant of FcepsilonRIbeta (beta(var)). We demonstrate that FcepsilonRIalpha is the core subunit with which the other subunits assemble strictly cotranslationally. In addition to alphabetagamma(2) and alphagamma(2), we demonstrate the presence of alphabeta and alphabeta(var)gamma(2) complexes that are stable in the detergent Brij 96. The role of individual FcepsilonRI subunits for the formation of functional, immunoglobulin E-binding FcepsilonRI complexes during endoplasmic reticulum (ER) assembly can be defined as follows: beta and gamma support ER insertion, signal peptide cleavage and proper N-glycosylation of alpha, whereas beta(var) allows accumulation of alpha protein backbone. We show that assembly of FcepsilonRI in the ER is a key step for the regulation of surface expression of FcepsilonRI. The ER quality control system thus regulates the quantity of functional FcepsilonRI, which in turn controls onset and persistence of allergic reactions.

The immunogenetics of asthma and eczema: a new focus on the epithelium

Asthma and eczema (atopic dermatitis) are the most common chronic diseases of childhood. These diseases are characterized by the production of high levels of immunoglobulin E in response to common allergens. Their development depends on both genetic and environmental factors. Over the past few years, several genes and genetic loci that are associated with increased susceptibility to asthma and atopic dermatitis have been described. Many of these genes are expressed in the mucosa and epidermis, indicating that events at epithelial-cell surfaces might be driving disease processes. This review describes the mechanisms of innate epithelial immunity and the role of microbial factors in providing protection from disease development. Understanding events at the epithelial-cell surface might provide new insights for the development of new treatments for inflammatory epithelial disease.

The E237G polymorphism of the high-affinity IgE receptor beta chain and asthma

BACKGROUND

The beta chain of high-affinity IgE receptor (FcepsilonRI beta) has been proposed as a candidate gene for asthma and atopic diseases.

OBJECTIVES

To determine the prevalence of the E237G polymorphism of the FcepsilonRI beta gene and to investigate its association with asthma and total IgE levels in 3 Asian populations.

METHODS

A total of 291 asthmatic patients (141 Chinese, 68 Malay, and 82 Indian) and 355 asymptomatic blood donors (157 Chinese, 100 Malay, and 98 Indian) were recruited. The E237G genotype was determined by allele-specific polymerase chain reaction. Total serum IgE level was measured by enzyme-linked immunosorbent assay.

RESULTS

The G allele was more common in Chinese controls (17.9%) than in Malay (11.5%) (P = .05) and Indian (9.2%) (P = .01) controls. Genotypes with the G allele were more prevalent in asthmatic patients in the Chinese population (odds ratio, 1.97; 95% confidence interval, 1.05-3.77; P = .04).

CONCLUSIONS

There were interethnic differences in the frequencies of the G variant among Chinese, Malay, and Indian populations. The E237G polymorphism of FcsRI beta may be a risk factor for asthma in the Chinese population.

Nonsense-mediated decay approaches the clinic

Nonsense-mediated decay (NMD) eliminates mRNAs containing premature termination codons and thus helps limit the synthesis of abnormal proteins. New results uncover a broader role of NMD as a pathway that also affects the expression of wild-type genes and alternative-splice products. Because the mechanisms by which NMD operates have received much attention, we discuss here the emerging awareness of the impact of NMD on the manifestation of human genetic diseases. We explore how an understanding of NMD accounts for phenotypic differences in diseases caused by premature termination codons. Specifically, we consider how the protective function of NMD sometimes benefits heterozygous carriers and, in contrast, sometimes contributes to a clinical picture of protein deficiency by inhibiting expression of partially functional proteins. Potential 'NMD therapeutics' will therefore need to strike a balance between the general physiological benefits of NMD and its detrimental effects in cases of specific genetic mutations.

The role of the FcepsilonRI beta-chain in allergic diseases

The high affinity receptor for IgE, FcepsilonRI, is a multimeric surface receptor that is expressed exclusively as a tetramer on rodent cells, but exists as a tetramer or trimer on human cells. The tetrameric form is expressed on effector cells of allergic responses such as mast cells and basophils and is composed of an IgE-binding alpha-subunit, a beta-subunit and a gamma-subunit dimer. Complexes lacking the beta-subunit are found on human antigen-presenting cells. On mast cells and basophils, FcepsilonRI is essential for IgE-mediated acute allergic reactions. Crosslinking of FcepsilonRI by IgE and multivalent antigen induces a signaling cascade that culminates in the release of preformed mediators and the synthesis of lipid mediators and cytokines. The beta-subunit functions as an amplifier of FcepsilonRI expression and signaling. As a consequence, strongly enhanced mast cell effector functions and in vivo allergic reactions can be observed in the presence of FcepsilonRIbeta. In contrast, a truncated beta-isoform (betaT) that is produced by alternative splicing acts as an inhibitor of FcepsilonRI surface expression. Thus, by producing two proteins with antagonistic functions, the FcepsilonRIbeta gene could serve as a potent regulator of allergic responses. In addition, the genomic region encompassing the beta-chain has been linked to atopy and a number of polymorphisms within the FcepsilonRIbeta gene are associated with various atopic diseases. It remains to be elucidated how these polymorphisms might affect the allergic phenotype. These functions of the beta-chain together with the described genetic linkages to atopy make it a candidate for a role in the pathophysiology of allergic diseases.

Nonsense-mediated mRNA decay: from vacuum cleaner to Swiss army knife

Nonsense-mediated mRNA decay (NMD) downmodulates mRNAs that have in-frame premature termination codons and prevents translation of potentially harmful truncated proteins from aberrant mRNAs. Two new approaches have identified physiological NMD substrates, and suggest that NMD functions as a multipurpose tool in the modulation of gene expression.

Fcgamma receptors on mast cells: activatory and inhibitory regulation of mediator release

Mast cell activation and subsequent release of proinflammatory mediators are primarily a consequence of aggregation of the high affinity receptors for IgE (FcepsilonRI) on the mast cell surface following antigen-dependent ligation of FcepsilonRI-bound IgE. However, data obtained from rodent and human mast cells have revealed that IgG receptors (FcgammaR) can both promote and inhibit mast cell activation. These responses appear to be species and/or mast cell phenotype dependent. In CD34+-derived human mast cells exposed to interferon-gamma, FcgammaRI is upregulated, FcgammaRII is expressed but not upregulated, and FcgammaRIII is not expressed. In contrast, in mouse mast cells, FcgammaRII and FcgammaRIII receptors are expressed, whereas FcgammaRI is not. Aggregation of FcgammaRI on human mast cells promotes mediator release in a manner generally similar to that observed following FcepsilonRI aggregation. Aggregation of FcgammaRIIb in mouse mast cells fails to influence cellular processes; however, when coligated with FcepsilonRI, signaling events thus activated downregulate antigen-dependent mediator release. These divergent responses are a consequence of different motifs contained within the cytosolic tails of the signaling subunits of these receptors and the specific signaling molecules recruited by these receptors following ligation. The studies described imply that data obtained in rodent models regarding the influence of FcgammaRs on mast cells may not be directly translatable to the human. The exploitation of FcgammaRs for a potential therapy for the treatment of allergic disorders is discussed in this context.

LD mapping of maternally and non-maternally derived alleles and atopy in FcepsilonRI-beta

Polymorphisms in the beta chain of the high affinity receptor for IgE (Fc epsilon RI-beta, MS4A2) are consistently associated with traits underlying asthma and atopy (immunoglobulin E-mediated allergy). However, the causal variants and haplotypes underlying disease have not yet been identified. Maternal effects, with association confined to maternally derived alleles, have been shown in some studies but not in others. We have therefore extended the known sequence and systematically detected polymorphisms across an 18.1 Kb genomic region that includes Fc epsilon RI-beta. Association testing in two panels of subjects showed the presence of single-nucleotide polymorphisms (SNPs) affecting prick skin tests and specific IgE responses in several clusters. Stepwise analyses indicated that the clusters represent independent effects. Interferon regulatory factor 2 (IRF-2) sites were altered by significantly associated SNPs in two regions. Strong association to maternally derived alleles was seen in one panel of subjects and not in the other. Maternal and non-maternally derived associations tended to share the same SNP clusters, but associations were stronger in the presence of maternal effects. Two regions of increased CpG concentration were identified in Fc epsilon RI-beta. One of these approximated a SNP cluster that showed strong association and maternal effects, providing a potential substrate for epigenetic effects.