Mechanisms of remission in oral immunotherapy
Interferons have diverse and often opposing roles in orchestrating immunological pathways. Recent studies from our group and others using a network analysis approach have found that type I interferons may also be important regulatory drivers in redirecting the allergic response towards remission of allergy following oral immunotherapy28,29 and may be negative regulators of the allergic CD4+ T cells response both in and outside of the treatment setting30,31. We examined gene co-expression networks in CD4+ T cells at study entry and following 18-months of Probiotic and Peanut Oral Immunotherapy in children who achieved remission following active treatment and placebo-treated controls who remained allergic. Results showed that remission following treatment was characterised by changes in the antigen-specific response to peanut, with loss of Th2 driven gene connectivity and replacement by a large integrated type I interferon network that incorporated Th2 genes within the module18. In contrast, a Th2 dominant module persisted in allergic children who received placebo treatment. Notably, the role of type I interferons has also been highlighted in the setting of subcutaneous immunotherapy (SCIT) for allergic rhinitis in adults. Persistent reduction of house dust mite (HDM) associated symptoms after SCIT treatment was associated with progressive integration of previously distinct type I interferon and Th2 gene modules, resulting in a rewired module in which the top nodes, ranked by degree of connectivity, were made up of type I interferon genes19. It is noteworthy that the same immune mechanisms were associated with disease remission across multiple allergen immunotherapy studies, despite major differences in the studies, including disease states and treatment modalities. This supports a role for type I interferon pathways as a fundamental mechanism through which lasting attenuation of allergen responsiveness is achieved following allergen immunotherapy. Both of these studies were conducted by profiling the total CD4+ T cell compartment, and future studies are needed to determine if the Th2 and IFN modules operate within a single CD4+ T cell population or whether these signals reflect changes in discrete cell subpopulations. In this context it is noteworthy that scRNAseq studies of CD4+ T cell memory responses to HDM have identified novel subsets of T-helper and T-regulatory cells, which express a type I interferon response signature, and are expanded in healthy non-allergic subjects, suggesting they may play a role in dampening allergic responses32. Further studies applying similar systems biology approaches to compare the effects of different therapies and clinical outcomes following treatment will further elucidate the underlying processes.
The precise mechanisms governing the interplay between type I IFN and Th2 responses in the context of allergen immunotherapy are unknown. Previous studies have demonstrated that type I IFNs can abrogate both the production of Th2 cytokines in antigen stimulated PBMC33 and expression of the high affinity IgE receptor34. Furthermore, type I interferons suppress the expression of GATA3 during differentiation of CD4+ T cells down a Th2 path and in fully committed CD4+ Th2 cells, and promotes epigenetic silencing of non-coding regions in the Th2 locus that controls Th2 cytokine expression35. Interferon genes (type I and type II) have also been shown to regulate a cluster of genes associated with levels of component resolved egg sIgG4 and sIgA after 8-months of egg OIT17.
Another regulatory mechanism that has been reported with OIT is T cell anergy. Expansion of the anergic (CD28-/CD38-/IFN-γ/IL4-/IL13-/IL10-) non-cytokine secreting T cell subset, as well as non-allergic (IFN-γ+) T cell types has been detected in those who achieve remission/SU (defined as absence of clinical reactivity at 3 months post treatment). Conversely, in those desensitised without remission/SU CD4+ T cell subsets were scattered across multiple CD4+ T cell phenotypes with only slight increases in anergic and non-allergic T cell phenotypes36. However, this finding was not replicated in a subsequent study by the same group when the frequency of peanut-specific T cells over the course of OIT was measured using Dextramers37. While shifts in the frequency of peanut-reactive T cell clonotypes may not be clearly linked to outcomes following OIT, the application of scRNAseq to this population has demonstrated a link between dampened Th2 and Th1 signatures in effector cells and remission21. Findings from this study were consistent with the findings that clonal anergy is linked with positive outcomes following OIT. Conversely, baseline inflammatory signals in Th1 and Th17 effector cells were associated with poorer outcomes following OIT21.
Another signal linked with clinical outcome following treatment is an early transient increase in TGF-β producing cells at one year into treatment37. This signal was detected in a mixed group of patients who either avoided the allergen in their diet leading up to the 3 month remission/SU challenge or continued on 300mg doses37. Therefore, it is unclear whether the finding relates to remission/SU or to desensitisation without remission/SU.
T regulatory cells play an instrumental role in the development and maintenance of oral tolerance38 and accordingly it is generally assumed that Treg must also play a role in remission of allergy in OIT39. Notably, pathogenic Tregs with a Th2-like phenotype have been described in murine models of food allergy and were also found to be circulating in the periphery of children with food allergy40. Functional studies from this work highlight that modulation of this population may promote the establishment of oral tolerance in food allergic individuals. Yet, evidence establishing Treg as primary mediators of remission following OIT in humans remains limited. Although two studies report changes to the antigen-specific Treg population following peanut OIT41,42, a more recent study profiling antigen-specific T cells with single-cell sequencing found no change in peanut-reactive Treg with OIT21. Moreover, a subset of peanut-reactive Treg with a Th2-like phenotype (Th2reg-like), matching a previously described population found in food allergic children40, was identified in this study. There is no evidence to support modulation of the frequency or phenotype of these cells with OIT, even in those who passed a food challenge 3-months after treatment and were classified as tolerant (remission)21. Induction of FOXP3 gene expression via demethylation of the FOXP3 has been linked with remission (defined as absence of clinical reactivity 3 months after treatment cessation, n=7) compared to those who failed to achieve remission (n=13), and this was reversed in those who lost their protection (n=4 participants who failed a challenge at six months post-treatment regained methylation of the FOXP3locus)41. These findings suggest that persistent activation of FOXP3 may be a critical requirement for lasting persistence of remission.