Cracking the Code: IPEX, FOXP3 and the Path to Gene Therapy

Discover how SR-TIGET scientists advanced the genetics of peripheral immune tolerance, from FOXP3 and IPEX to gene therapy using lentiviral vectors.

The discovery of the FOXP3 gene and its role in the autoimmune syndrome IPEX marked a turning point in the understanding of immune regulation. What began as fundamental research into the biology of regulatory T cells (Tregs) soon evolved also into a clinical endeavour to study and correct immune dysfunction at its genetic roots — and SR-TIGET has been at the forefront of this translational research.

The identification of FOXP3 mutations as the cause of IPEX (Immunodysregulation Polyendocrinopathy Enteropathy X-linked) not only revealed the molecular basis of a devastating childhood disease, but also provided a key to decoding immune tolerance itself.
Children with IPEX develop severe autoimmune symptoms within the first months of life — inflammation of the intestine, autoimmune diabetes, and multi-organ immune dysregulation — due to a single gene defect that disrupts Treg function.

At SR-TIGET, Rosa Bacchetta and Maria Grazia Roncarolo spearheaded studies investigating the mechanisms linking FOXP3 mutations to IPEX pathogenesis. Their work laid the foundation for gene therapy approaches designed to restore immune balance by correcting the underlying genetic defect.

After years of pre-clinical work, Rosa Bacchetta — who led IPEX studies at SR-TIGET and now works at Stanford University — launched the first academic, first-in-human Phase I clinical trial (NCT05241444) testing a lentiviral gene therapy for IPEX. The approach, originally developed with the support of Fondazione Telethon and in collaboration with Luigi Naldini, who succeeded Maria Grazia Roncarolo as SR-TIGET Director in 2008, uses lentiviral vectors carrying a functional copy of the FOXP3 gene to correct Treg dysfunction in IPEX patients’ cells. By restoring FOXP3 expression, these engineered T cells recover their regulatory properties, potentially offering a therapeutic strategy for this severe autoimmune disease.

The FOXP3 overexpression strategy has also prompted novel approaches in immunotherapy research. It inspired scientists to reprogram conventional T cells into regulatory ones, and to design CAR- and TCR-engineered Tregs capable of recognising specific antigens — a breakthrough that could transform treatment approaches for complex autoimmune disorders such as type 1 diabetes, systemic lupus erythematosus, myasthenia gravis, inflammatory myopathies, systemic sclerosis, neuromyelitis optica spectrum disorder, and multiple sclerosis.

Moreover, Roncarolo’s work has been highly relevant for gene therapy as inducing immune tolerance to the transgene is essential, especially in immunocompetent patients. Insights from Roncarolo’s studies, coupled with the pioneering expertise of SR-Tiget in gene therapy, have advanced the development of lentiviral vectors designed to minimise antigen presentation by professional antigen-presenting cells, allowing the transgene to persist by promoting Tregs - an approach advanced by Andrea Annoni, Brian Brown, Alessio Cantore, and Naldini

This innovation not only increased the safety and efficacy of gene therapy in immunocompetent patients but also strengthened SR-TIGET’s reputation as a global leader in vector design and immune-tolerance research.

While gene therapy was advancing, SR-TIGET researchers also explored how to expand Tregs ex vivo, as they are very scarce in the peripheral blood. Manuela Battaglia and Maria Grazia Roncarolo discovered that rapamycin, a well-known immunosuppressive drug, could instead act as an immunomodulator, selectively promoting the expansion of functional Tregs while limiting the proliferation of conventional effector T cells. Their 2006 landmark study demonstrated that rapamycin enables the ex vivo expansion of functional Tregs suitable for clinical use in autoimmune diseases such as type 1 diabetes.

Today, protocols based on rapamycin are considered the gold standard for Treg expansion ex vivo and are used worldwide in clinical trials to prevent organ transplant rejection.

Together, these discoveries illustrate how SR-TIGET’s scientific ecosystem has always had the vision of integrating diverse approaches toward a single goal. By combining the genetic repair of Tregs with strategies to enhance their numbers and function, SR-TIGET scientists have helped pave the way for a new generation of targeted immunotherapies.