Perez Group@illinois

The genome editing revolution that occurred in the past 5 years has been possible through the development of different types of synthetic DNA binding domains that can be readily modified to customize their specificity. These DNA binding domains can be fused with different effector domains to implement targeted changes in genomic DNA.

The nature of these changes can be, for instance, 1) Introduction of a double-strand break for targeted modification of a given genomic DNA sequence, 2) Recruitment of the transcriptional initiation complex for up-regulation of native gene expression, 3) Recruitment of chromatin remodeling enzymes for gene silencing, and 4) epigenetic modification of DNA genomic sequences for permanent and hereditable changes in gene expression.

Importantly, these changes can be performed in vivo and in most organisms, thus allowing us to redefine life. Our lab is focused in further developing genome editing technologies and their application in gene therapy, tissue engineering and biopharmaceutical production.

Gene Therapy

There are over 300 well-characterized diseases caused by mutations in single genes. Several genome editing tools have been developed that have the potential to cure or ameliorate the devastating consequences of these genetic errors. Examples include Duchenne muscular dystrophy, sickle cell disease, or hemophilia among others. Diseases inherited as complex traits, such as heart disease, Alzheimer's disease, or diabetes, are far more common in the population. Because of the multifactorial nature of these diseases, they are difficult to target. However, the genome-wide association studies performed in the past decade have identified genetic elements with causative roles that are good candidates for therapeutic intervention. We are developing gene therapy approaches to treat both monogenic diseases and diseases with complex traits.

Tissue Engineering

Embryonic stem cells can be differentiated into specialized cells with specific functions, such as brain cells, blood cells, heart muscle or bone. Because they can be used to regenerate and repair diseased or damaged tissues in patients, they have been portrayed as a potential cure for a variety of conditions and disabilities. However, major problems in stem cell research and tissue engineering persist such as, efficient generation of stem cells, efficient differentiation of cells into target tissues and survival and integration of the implant into the recipient. We are using synthetic biology approaches to increase the efficiency and decrease the cost associated with the use of stem cells for tissue engineering.

Strain Development for Drug Manufacturing

The yeast Pichia pastoris has become a popular and highly efficient system for the production of heterologous proteins. The most significant advantages of this yeast compared with other expression system are ability to growth to very high densities, capacity to produce and secrete heterologous proteins into the growth medium at high levels, low level of secretion of native proteins into the growth medium, and glycosylation patterns similar to those found in humans. However, proper expression of different proteins requires extensive genetic engineering to achieve the desired levels of expression. We are developing synthetic biology toolkits for efficient strain development of this yeast and other unconventional expression systems.