Dual transcriptomic and epigenomic study of reaction severity in peanut-allergic children

BACKGROUND

Unexpected allergic reactions to peanut are the most common cause of fatal food-related anaphylaxis. Mechanisms underlying the variable severity of peanut-allergic reactions remain unclear.

OBJECTIVES

We sought to expand mechanistic understanding of reaction severity in peanut allergy.

METHODS

We performed an integrated transcriptomic and epigenomic study of peanut-allergic children as they reacted in vivo during double-blind, placebo-controlled peanut challenges. We integrated whole-blood transcriptome and CD4+ T-cell epigenome profiles to identify molecular signatures of reaction severity (ie, how severely a peanut-allergic child reacts when exposed to peanut). A threshold-weighted reaction severity score was calculated for each subject based on symptoms experienced during peanut challenge and the eliciting dose. Through linear mixed effects modeling, network construction, and causal mediation analysis, we identified genes, CpGs, and their interactions that mediate reaction severity. Findings were replicated in an independent cohort.

RESULTS

We identified 318 genes with changes in expression during the course of reaction associated with reaction severity, and 203 CpG sites with differential DNA methylation associated with reaction severity. After replicating these findings in an independent cohort, we constructed interaction networks with the identified peanut severity genes and CpGs. These analyses and leukocyte deconvolution highlighted neutrophil-mediated immunity. We identified NFKBIA and ARG1 as hubs in the networks and 3 groups of interacting key node CpGs and peanut severity genes encompassing immune response, chemotaxis, and regulation of macroautophagy. In addition, we found that gene expression of PHACTR1 and ZNF121 causally mediates the association between methylation at corresponding CpGs and reaction severity, suggesting that methylation may serve as an anchor upon which gene expression modulates reaction severity.

CONCLUSIONS

Our findings enhance current mechanistic understanding of the genetic and epigenetic architecture of reaction severity in peanut allergy.

T-independent IFNγ and B cells synergize to prevent mortality associated with disseminated Chlamydia muridarum genital infection

CD4 T cells and antibody are required for optimal acquired immunity to C. muridarum genital tract infection, and T cell-mediated IFNγ production is necessary to clear infection in the absence of humoral immunity. However, the role of protective T cell-independent immune responses against primary infection remain unclear. We addressed this problem by inoculating wild-type and immune-deficient mice with a plaque-purified strain (CM001) isolated from C. muridarum Nigg stock capable of enhanced extragenital replication. Genital CM001 inoculation resulted in transient dissemination to the lungs and spleen in wild-type mice prior to clearance. However, CM001 genital infection induced lethality in STAT1−/− and IFNG−/− mice, where IFNγ signaling is absent, and in Rag1−/− mice that lack T and B cells but are competent for innate IFNγ signaling. In contrast, muMT, nude, and Tcra−/− mice survived. These data collectively indicate that IFNγ prevents lethal CM001 infection in the absence of T cells and suggest a B cell co-requirement for protection. Adoptive transfer of convalescent immune sera, but not naïve IgM antibody, to Rag1−/− mice significantly increased survival time and transfer of naïve B cells completely rescued Rag1−/− mice against CM001 lethality. Protection was associated with a significant reduction in the lung chlamydial burden of genitally infected mice. These data reveal an important synergism between T-independent B cell responses and innate IFNγ in chlamydial host defense, and suggest cooperative interactions between T-independent IgG and IFNγ are essential for limiting extragenital dissemination.

A novel mutation in IFN-gamma receptor 2 with dominant negative activity: biological consequences of homozygous and heterozygous states

We identified two siblings homozygous for a single base pair deletion in the IFN-gammaR2 transmembrane domain (791delG) who presented with multifocal Mycobacterium abscessus osteomyelitis (patient 1) and disseminated CMV and Mycobacterium avium complex infection (patient 2), respectively. Although the patients showed no IFN-gammaR activity, their healthy heterozygous parents showed only partial IFN-gammaR activity. An HLA-identical bone marrow transplant from the mother led patient 1 to complete hemopoietic reconstitution, but only partial IFN-gammaR function. We cloned and expressed fluorescent fusion proteins of the wild-type IFN-gammaR2, an IFN-gammaR2 mutant previously described to produce a complete autosomal recessive deficiency (278del2), and of 791delG to determine whether the intermediate phenotype in the 791delG heterozygous state was caused by haploinsufficiency or a dominant negative effect. When cotransfected together with the wild-type vector into IFN-gammaR2-deficient fibroblasts, the fusion protein with 791delG inhibited IFN-gammaR function by 48.7 +/- 5%, whereas fusion proteins with 278del2 had no inhibitory effect. Confocal microscopy of 791delG fusion proteins showed aberrant diffuse intracellular accumulation without plasma membrane localization. The fusion protein created by 791delG did not complete Golgi processing, and was neither expressed on the plasma membrane, nor shed extracellularly. The mutant construct 791delG exerts dominant negative effects on IFN-gamma signaling without cell surface display, suggesting that it is acting on pathways other than those involved in cell surface recognition of ligand.