Identification of unstable regulatory and autoreactive effector T cells that are expanded in patients with <i>FOXP3</i> mutations
Šimon Borna, Esmond Lee, Jason Nideffer, Akshaya Ramachandran, Bing Wang, Jeanette Baker, Melissa Mavers, Uma Lakshmanan, Mansi Narula, Amy Kang-hee Garrett, Janika Schulze, Sven Olek, Louis Marois, Yaël Gernez, Monica Bhatia, Hey Chong, Jolán E. Walter, Maleewan Kitcharoensakkul, Abigail Lang, Megan A. Cooper, Alice Bertaina, Maria Grazia Roncarolo, Eric Meffre, Rosa Bacchetta
Abstract
Studies of the monogenic autoimmune disease immunodysregulation polyendocrinopathy enteropathy X-linked syndrome (IPEX) have elucidated the essential function of the transcription factor FOXP3 and thymic-derived regulatory T cells (T regs ) in controlling peripheral tolerance. However, the presence and the source of autoreactive T cells in IPEX remain undetermined. Here, we investigated how FOXP3 deficiency affects the T cell receptor (TCR) repertoire and T reg stability in vivo and compared T cell abnormalities in patients with IPEX with those in patients with autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy syndrome (APECED). To study T regs independently of their phenotype and to analyze T cell autoreactivity, we combined T reg -specific demethylation region analyses, single-cell multiomic profiling, and bulk TCR sequencing. We found that patients with IPEX, unlike patients with APECED, have expanded autoreactive T cells originating from both autoreactive effector T cells (T effs ) and T regs . In addition, a fraction of the expanded T regs from patients with IPEX lost their phenotypic and functional markers, including CD25 and FOXP3. Functional experiments with CRISPR-Cas9–mediated FOXP3 knockout T regs and T regs from patients with IPEX indicated that the patients’ T regs gain a T H 2-skewed T eff -like function, which is consistent with immune dysregulation observed in these patients. Analyses of FOXP3 mutation-carrier mothers and a patient with IPEX after hematopoietic stem cell transplantation indicated that T regs expressing nonmutated FOXP3 prevent the accumulation of autoreactive T effs and unstable T regs . These findings could be directly used for diagnostic and prognostic purposes and for monitoring the effects of immunomodulatory treatments.