Functional characterization of the atopy-associated gene PHF11

doi:10.1016/j.jaci.2008.02.028

Journal of Allergy and Clinical Immunology

Volume 121, Issue 5, May 2008, Pages 1148-1154.e3

https://doi.org/10.1016/j.jaci.2008.02.028 Get rights and content

Background

Polymorphisms in the plant homeodomain finger protein 11 gene (PHF11) are associated with increased total serum IgE levels, asthma, and severe atopic dermatitis (AD) in children. Although PHF11 includes a plant homeodomain, a motif often found in transcriptional regulators, the function of PHF11 has not been investigated.

Objective

We sought to test (1) whether PHF11 regulates the transcription of genes involved in allergic disorders and (2) whether polymorphisms in PHF11 predict changes in the expression or function of this gene.

Methods

Microarray analysis was used to examine the expression of PHF11 in different immune cell subsets, and the function of PHF11 was tested by using small interfering RNA–induced knockdown or overexpression of PHF11 in primary CD4⁺ T cells or Jurkat T cells. Genotype-dependent effects on PHF11 expression were tested by using an allele-specific gene expression, and the transcriptional activity of PHF11 was determined by using luciferase hybrid gene reporter assays and in vitro DNA-binding electromobility shift assays.

Results

PHF11 expression was higher in T_H1 cells relative to that in T_H2 cells, and knockdown of PHF11 expression reduced expression of the T_H1-type cytokines IFN-γ and IL-2. The G-allele of a 3′ untranslated region polymorphism associated with AD was correlated with reduced abundance of PHF11 RNA in T_H1 cells, as well as an increase in a PHF11 isoform lacking exon II. Evidence was also found for a physical and functional interaction between PHF11 and the p65 subunit of nuclear factor κB.

Conclusion

PHF11 is a regulator of T_H1-type cytokine gene expression. The reduction in PHF11 expression seen with an AD-associated genotype could contribute to the strong T_H2 responses that characterize many allergic individuals.

Section snippets

Methods

Additional methods for T_H1 and T_H2 cultures, cDNA synthesis and cloning, and immune precipitation assays and details of the antibodies used in this study appear in the Methods section of the Online Repository at www.jacionline.org.

Results

Using a well-characterized dataset of gene expression profiles from T cells, B cells, and other immune cells,9, 10 we found robust PHF11 expression in B- and T-cell subsets, including peripheral blood central (CCR7⁺CD4⁺CD45RO⁺) and effector (CCR7⁻CD4⁺CD45RO⁺) memory T cells. In the context of allergy, perhaps the most interesting result was the differential expression of PHF11 between T_H1 and T_H2 cells generated from neonatal CD4⁺ T cells, with the highest expression seen in T_H1 cells (Fig 1, A

Discussion

In this article we show that (1) PHF11 expression is higher in T_H1 than in T_H2 cells; (2) siRNA knockdown of endogenous PHF11 or overexpression of PHF11 either decreased or increased the expression of T_H1-type genes, respectively; (3) The G allele of the 3′UTR SNP rs1046295 that is preferentially transmitted to children with AD was associated with decreased PHF11 RNA in T_H1 cells, and a predicted nonfunctional PHF11 isoform lacking exon II was more common in individuals carrying this G allele;

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Cited by (27)

Analysis of microbiota reveals the underlying mechanism of PHF11 in the development of Enterococcus-regulated endometriotic cysts
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Endometriosis (EMS) is a prevalent disease and the etiologies has not uniform. Microbiota is associated with human diseases. To delve into the relationship between EMS and microbiota, Ectopic (EM) and eutopic (EU) endometrial tissues, pharyngeal swabs, and stools were collected from EMS patients. The microbiota composition of EM and EU partially overlapped, with similar taxon numbers and diversity, but the richness levels were significantly different. A comparison of intestinal microbes in healthy individuals (FN) and EMS patients (FE) revealed that the richness of Enterococcus, Pseudomonas, Haemophilus, and Neisseria was enhanced in FE. In addition, Enterococcus-induced mice (EFA) presented with a higher degree of lesion infiltration and a wider distribution of lesions. Proteomic analysis revealed the expression of plant homeodomain finger 11 (PHF11) was notably downregulated in EFA. And the downregulated expression of PHF11 was accompanied by the upregulated expression of interleukin 8 (IL-8). Our findings suggest a potential regulatory mechanism for PHF11 in EMS development.
From gene identifications to therapeutic targets for asthma: Focus on great potentials of TSLP, ORMDL3, and GSDMB
2023, Chinese Medical Journal Pulmonary and Critical Care Medicine
Asthma is a chronic respiratory disease, and clinically, asthma exacerbations remain difficult to treat. The disease is caused by combinations of and interactions between genetic and environmental factors. Genomic and genetic approaches identified many novel genes to treat asthma and brought new insights into the disease. The products of the genes have functional roles in regulating physiological or pathophysiological processes in airway structural cells and immune system cells. Genetic factors also interact with environmental factors such as air pollutants, and bacterial and viral infections to trigger the disease. Thymic stromal lymphopoietin (TSLP), orosomucoid-like 3 (ORMDL3), and gasdermin B (GSDMB) are three genes identified by genetic studies to have a great potential as therapeutic targets of asthma. TSLP is an important driver of type 2 inflammation. ORMDL3 mediates cell stress, sphingolipid synthesis, and viral and bacterial infections. GSDMB regulates cell pyroptosis through its N and C terminals and can bind sulfatides to influence inflammatory response. Investigating inhibitors or modulators for these pathways would bring a new landscape for therapeutics of asthma in future.
Allele-specific transcription of the asthma-associated PHD finger protein 11 gene (PHF11) modulated by octamer-binding transcription factor 1 (Oct-1)
2011, Journal of Allergy and Clinical Immunology
Citation Excerpt :
Studies of rs1046295 have shown the G allele to be associated with both increased IgE levels13 and asthma.39 Based on the results presented here and by Clarke et al,59 this may be a result of decreased expression and alternative splicing caused by the G allele because of differential binding of transcription factors. The chromosome 13q14 locus modulates total serum IgE levels, raised amounts of which are a main feature of atopic diseases such as asthma.
Asthma is a common, chronic inflammatory airway disease of major public health importance with multiple genetic determinants. Previously, we found by positional cloning that PHD finger protein 11 (PHF11) on chromosome 13q14 modifies serum immunoglobulin E (IgE) concentrations and asthma susceptibility. No coding variants in PHF11 were identified.
Here we investigate the 3 single nucleotide polymorphisms (SNPs) in this gene most significantly associated with total serum IgE levels—rs3765526, rs9526569, and rs1046295—for a role in transcription factor binding.
We used electrophoretic mobility shift assays to examine the effect of the 3 SNPs on transcription factor binding in 3 cell lines relevant to asthma pathogenesis. Relative preferential expression of alleles was investigated by using the allelotyping method.
Electrophoretic mobility shift assays show that rs1046295 modulates allele-specific binding by the octamer-binding transcription factor 1 (Oct-1). Analysis of the relative expression levels of the 2 alleles of this SNP in heterozygous individuals showed a modest, but highly significant (P = 6.5 × 10⁻¹⁶), preferential expression of the A allele consistent with a functional role for rs1046295.
These results suggest a mechanism by which rs1046295 may act as a regulatory variant modulating transcription at this locus and altering asthma susceptibility.
The PHF11 gene is not associated with asthma or asthma phenotypes in two independent populations
2009, Thorax
Numerous areas of the human genome have previously been associated with asthma and asthma-related phenotypes, but few positive findings have been successfully replicated in independent populations. Initial studies have reported strong associations of variants in the plant homeodomain zinc finger protein 11 (PHF11) gene with serum IgE levels, asthma, airway hyper-responsiveness and childhood atopic dermatitis. Objectives: To investigate the association of variants in the PHF11 gene with asthma and associated intermediate phenotypes in two independent Western Australian population-based samples.
A linkage-disequilibrium (LD)-tagging set of 20 single nucleotide polymorphisms (SNPs) was genotyped in PHF11 in two separate populations (total n = 2315), a family-based twin study consisting of 230 families (n = 992 subjects) and a population-based nested case-control study consisting of 617 asthma cases and 706 controls. Information regarding asthma, respiratory physiology, atopy and environmental exposures was collected. Transmission disequilibrium tests, variance components models and generalised linear models were used to test for association between PHF11 SNPs and selected asthma outcomes (including longitudinal change in lung function).
After correction for multiple testing, no statistically significant (p<0.05) associations were found between PHF11 and either asthma or total serum IgE levels in either population. No statistically significant associations were found with any other asthma-associated phenotypes in either population.
Previously reported associations of PHF11 with asthma outcomes were not replicated in this study. This study suggests that PHF11 is unlikely to contain polymorphic loci that have a major impact on asthma susceptibility in our populations.
Microglial synaptic pruning in the nucleus accumbens during adolescence sex-specifically influences splenic immune outcomes
2023, bioRxiv
Single-cell characterization of a model of poly I:C-stimulated peripheral blood mononuclear cells in severe asthma
2021, Respiratory Research

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: Supported by a grant from the National Health and Medical Research Council of Australia.

: Disclosure of potential conflict of interest: M. S. Rolph has received research support from the National Health and Medical Research Council of Australia. G. J. Stewart has received research support from the National Health and Medical Research Council of Australia, the Australian Research Council, and Multiple Sclerosis Research Australia. G. J. Jones has received research support from the University of Sydney and the National Health and Medical Research Council of Australia. The rest of the authors have declared that they have no conflict of interest.

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The Editors' choiceFunctional characterization of the atopy-associated gene PHF11

Background

Objective

Methods

Results

Conclusion

Section snippets

Methods

Results

Discussion

J Allergy Clin Immunol

J Allergy Clin Immunol

J Allergy Clin Immunol

Lancet

Trends Biochem Sci

J Allergy Clin Immunol

J Immunol Methods

Immunity

J Mol Biol

Mol Cell

Impaired interferon-gamma production in a subset population of severe atopic dermatitis

Int Arch Allergy Immunol

Polymorphisms within the PHF11 gene at chromosome 13q14 are associated with childhood atopic dermatitis

Genes Immun

Positional cloning of a quantitative trait locus on chromosome 13q14 that influences immunoglobulin E levels and asthma

Nat Genet

Identification of T cell-restricted genes, and signatures for different T cell responses, using a comprehensive collection of microarray datasets

J Immunol

T follicular helper cells express a distinctive transcriptional profile, reflecting their role as non-Th1/Th2 effector cells that provide help for B cells

J Immunol

The Editors' choice
Functional characterization of the atopy-associated gene PHF11