A proactive missense variant atlas for the Autoimmune Regulator

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Project Summary/Abstract Pathogenic variants of the Autoimmune Regulator (AIRE) gene cause the primary immunodeficiency disease Autoimmune Polyendocrine Syndrome Type 1 (APS-1; also called Autoimmune Polyendocrinopathy with Candidiasis and Ectodermal Dystrophy), which manifests as symptoms including chronic mucocutaneous candidiasis, hypoparathyroidism, and Addison’s disease among other autoimmune symptoms. AIRE prevents autoimmunity by increasing the expression of tissue-specific genes in the niche of developing T cells, allowing for the elimination of emerging self-reactive T-cells before they can mature. Sequencing of AIRE is an increasingly common tool to diagnose APS-1, and earlier diagnosis can benefit patients. However, diagnosis is limited by the fact that two thirds of variants are missense, and that more than half of the missense variants found are “of unknown significance”. Testing the function of variants in cultured cells can provide strong evidence for more informative variant classification, but these tests are carried out reactively, often months or years after a new variant is first observed in a patient. A proactive solution to this problem is to efficiently assess the function of all possible missense variants to generate a sequence-function map. Such maps can provide immediate and accurate evidence to diagnose disease, even for never-before-seen variants. We have developed and validated one scalable assay for testing AIRE missense variants, using human cells with a fluorescent reporter of insulin promoter activity, and are exploring other scalable assays. We will: 1) Generate a sequence-function map to enable more accurate clinical interpretation of AIRE missense variants and; 2) Validate and characterize the AIRE sequence-function map. A sequence-function map of AIRE will provide key proactive evidence for rapid and definitive genetic diagnosis of APS-1, and ultimately more positive patient outcomes.