2012 Annual Report

Correcting genes that cause inherited diseases

Drs. Amanda Mak and Barry Stoddard

Using a unique form of computational and X-ray crystallographic analyses, Dr. Barry Stoddard's team of researchers, including Drs. Phil Bradley and Amanda Mak, solved the structure of a unique type of DNA-targeting protein. This will enable them to engineer the protein to fix genetic diseases, such as sickle cell anemia and cystic fibrosis.


In his Hutchinson Center laboratory, structural biologist Dr. Barry Stoddard is engineering biochemical guided missiles to fix genetic diseases.

After almost 20 years analyzing unique types of proteins that seek out and bind to precise gene targets, Stoddard’s laboratory made a potentially lifesaving breakthrough this year, which they immediately began translating into tools to provide better care for patients.

Stoddard and his team of researchers were able to take this leap forward when they determined the three-dimensional structure of a protein called a TAL effector—transcription-activator-like effector— which, along with a group of DNA-targeting enzymes called homing endonucleases, can be used to treat genetic diseases. Stoddard and colleagues are now attempting to do just that, by combining both types of proteins to potentially treat and cure inherited disorders, such as cystic fibrosis and sickle cell anemia through a technique known as targeted gene correction.

Already, he’s collaborating with Dr. M.A. Bender to develop therapies for sickle cell anemia—a devastating blood disorder that causes excruciating pain and leads to a host of chronic, sometimes fatal health problems.

Bender, an affiliate researcher at the Hutchinson Center, is an associate professor of pediatrics at the University of Washington and director of the sickle cell clinic at Odessa Brown Children’s Clinic. After Bender identified a DNA sequence associated with the disease, Stoddard engineered a targeting protein to moderate the genetic defect.

Targeting sickle cell is just the first step. By determining the TAL effector structure, Stoddard has opened the door to alter the protein for a variety of biotech and medical applications. “The upcoming years will see an explosion in the development and use of TAL effectors for corrective gene therapy,” he said.

Although still in the developmental stage, targeted gene correction is a giant advance from existing gene therapy, which involves introducing a corrected version of a defective, disease-causing gene with the hope that it assumes the role of the defective gene. The problem is that the corrected gene doesn’t always find its way to a safe or useful location in a patient’s DNA—a drawback that limits the therapeutic benefits and can cause harmful side effects.

Targeted gene correction with TAL effectors involves directly repairing disease-causing genes, which promises more predictable results without harmful side effects because the TAL effector can lock onto precisely the right gene.

In nature, TAL proteins exist in a type of bacteria that infects plants such as soybeans, tomatoes and peppers. The bacteria use them to target specific DNA sites in the plants.

Stoddard’s breakthrough enables scientists to see exactly how TAL effectors recognize specific DNA sequences and bind to them. “By solving their structure, we can manipulate TAL effectors to find human DNA targets, stay active longer, or deliver additional molecules that drive a desired change in the gene target,” he said.

This is exactly what Stoddard envisioned when he began studying gene targeting proteins almost 20 years ago—and what he and Bender are doing to correct the genetic defect that causes sickle cell anemia.

“We’re getting close to being able to test it on human cells in the lab. If it works, we’ll move forward with improved versions,” said Bender. “Our ultimate hope is that we can dramatically reduce the symptoms of sickle cell anemia—and possibly even provide a cure.”

Dr. Barry Stoddard’s advances in targeted gene correction were made possible in part by a generous gift from the Cuyamaca Foundation.

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