Background/Purpose: Vitamin A and its major metabolite, retinoic acid (ATRA), modulate T cell function and fitness to shape immune responses. Vitamin A deficiency causes increased susceptibility to infection, leading to the death of an estimated 250,000-600,000 children per year. Osteoarthritis has been linked to variants in the ALDH1A2 gene, which metabolizes Vitamin A to ATRA. Retinoic acid is an essential positive regulator of T effector cell responses, yet retinoids can also dampen immune responses through inhibition of effector cytokine production. Moreover, ATRA induces expression of the transcription factor Foxp3, which is necessary for immune tolerance. This multifaceted effect of ATRA complicates dissection of the molecular mechanisms that elicit negative immunoregulatory functions.

Methods: We aimed to evaluate the direct effects of retinoic acid induced immunomodulation that are not dependent on enhancing T regulatory cell function. We performed RNA-seq and compared the transcriptomes of ATRA-treated and untreated T helper cell subsets. We used Chromatin Immunoprecipitation-sequencing (ChIP-seq) and Assay for Transposase-Accessible Chromatin-sequencing (ATAC-seq) to characterize ATRA-induced changes in chromatin architecture.

Results: We characterized an ATRA-regulated gene signature that was independent of CD4 T cell subset. We identified IL-9 as the cytokine whose gene expression is most strongly inhibited. Using Foxp3-mutant (Scurfy) mice, we demonstrated that ATRA’s immunomodulatory effects, including IL-9 inhibition, are Foxp3-independent. We confirmed that retinoic acid potently inhibits IL-9 in T cells in vitro, and in T cells and Type 2 innate lymphoid cells (ILC2s) in an in vivo model of allergic lung disease. We mapped chromatin accessibility of the Il9 locus by ATAC-seq and enhancer marks by ChIP-seq, which led us to identify several novel Il9 enhancers. We observed that RAR-alpha binds directly to the Il9 locus, reduces chromatin accessibility, and disrupts looping between the Il9 promoter and associated enhancers.

Conclusion: Our observation suggests that ATRA-RAR-alpha directly suppresses IL-9 by modifying enhancer architecture, which may serve as a paradigm for the mechanism by which retinoic acid modulates cytokine expression.

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ACR Meeting Abstracts - https://acrabstracts.org/abstract/retinoic-acid-inhibits-expression-of-interleukin-9-by-altering-enhancer-architecture/