Bridging The Gap
SPARKing approaches to treat a rare disease
February 27, 2020
Rare diseases are a conundrum. While over 20 million individuals are affected in the U.S., each rare disease only affects a small number of patients. As a result, little is known about each disease and few have approved therapies.
IPEX (Immunodysregulation polyendocrinopathy enteropathy X-linked) syndrome is one of these. It’s a monogenetic, X-linked disease that results from mutations in FOXP3, a master gene for regulatory T cell, or Treg, development and function. While only one gene is affected, multiple different types of mutations to FOXP3 in the patient population lead to a large spectrum of clinical manifestations. This makes it difficult to diagnose and understand the disease.
Dr. Rosa Bacchetta, associate professor of pediatrics – stem cell transplantation, explained that when FOXP3 is mutated, the protein is still expressed, but the level and function can vary based on mutation. As FOXP3 is a transcription factor that interacts with many different genes, “there is so much heterogeneity in how severe the disease is and how it is manifested.”
IPEX syndrome typically manifests at or near birth, exclusively in males. FOXP3 mutations result in dysregulated immune response and autoimmune attack on organs, especially gut, pancreas and skin, and can be fatal within one year if not diagnosed and treated.
As a physician, Bacchetta and the Stem Cell Transplantation Team have treated IPEX syndrome patients at Stanford, and her research focuses on understanding the pathogenesis of the disease and identifying new treatments.
IPEX disease is currently treated either with immunosuppressive drugs or with an allogeneic hematopoietic cell transplant. However, pharmacological immunosuppression isn’t always effective, and comes with inevitable side effects. Not every patient has a compatible donor for transplantation, and patients are sensitive to conditioning regimens.
Bacchetta is working on two approaches to treat the disease that could be longer-lasting with fewer side effects – one, a T cell gene therapy approach, as well as CRISPR-based gene editing in stem cells, a project supported by SPARK.
Bacchetta’s first approach is to use a lentivirus to transfer the FOXP3 gene into a patient’s own T cells ex vivo, restoring function to the Tregs, which then are infused back to the patient.
Her team is also investigating the use of CRISPR-Cas9 gene editing to insert FOXP3 into autologous hematopoietic stem cells (HPSCs), which would differentiate into fully functional Tregs. A successful stem cell transplant with these gene-edited cells could cure the disease.
SPARK selected Bacchetta’s IPEX project for funding and support in 2016.
Bacchetta credits SPARK for getting the CRISPR-based gene editing project off the ground. “SPARK has been extremely supportive. I started this project thanks to SPARK funding,” she said.
SPARK co-director Kevin Grimes said the program selected Bacchetta’s project for several reasons. “Children with IPEX syndrome are in great need of better treatment options, and Rosa’s approach is both scientifically compelling and feasible to develop. Also, since IPEX syndrome is an ultra-rare disease, there is little economic incentive for the biopharmaceutical industry to work on novel therapies. As part of a non-profit academic institution, SPARK can support important new treatments regardless of financial outcomes.”
Bacchetta thinks gene editing will be an ideal strategy for effective gene therapy in IPEX syndrome. FOXP3 is differentially regulated within lymphocytes – it is highly expressed on some CD4+ T cells, but expressed at low levels and transiently on other lymphocytes. “It is difficult to reproduce that differential regulation with gene therapy, unless you replace the gene maintaining all the endogenous regulatory regions intact,” Bacchetta said.
The team has data showing that CRISPR-edited HPSCs engraft and differentiate in humanized mouse models. The edited cells are generating normal T cells with differential regulation, Bacchetta said, and the team is seeing restoration of up to 50% of normal expression.
The T cell gene therapy project is currently undergoing IND enabling studies with the goal of beginning clinical trials in 2021. The project received a $5.5 million CIRM grant last year, and is one of the main projects in the pipeline of the Center for Definitive and Curative Medicine, which Bacchetta is part of.
Bacchetta’s CRISPR-based gene editing project is currently in preclinical testing. Bacchetta also received a faculty scholar grant from MCHRI in September to support the project. A manuscript has been provisionally accepted in a major peer-reviewed journal.
The project was initially solely funded by SPARK, which allowed Bacchetta to build the preliminary results to get additional funding and support the research behind the publication.
Bacchetta said that there are additional advantages that SPARK provides, such as its network. “It’s very useful that we have presentations at SPARK, where we can discuss our work” with industry advisers such as regulatory experts, she said. Bacchetta also credits co-directors Grimes and Daria Mochly-Rosen’s help by inviting her to present data at conferences and connecting her with companies and donors.