A Cambridge startup is using bacteria to deliver the promise of RNAi therapeutics.

Rachael Moeller Gorman

RNA interference (RNAi) is a natural process in cells that silences genes. Harnessing this process by designing RNA molecules to turn off specific genes involved in disease could offer a powerful new kind of drug. But scientists have struggled to figure out how to efficiently deliver these molecules to the right cells in humans. One local startup believes it has found a promising approach: bacteria.

Eight-month-old Cequent Pharmaceuticals, based in Cambridge, uses engineered nonpathogenic E. coli to create short hairpin RNA (shRNA) and deliver them into tissues that are easily colonized by bacteria, such as the gut lining. Without the bacteria to act as a carrier, the RNA would need to be chemically modified or encapsulated in some way to be able to pass through cell membranes; synthesizing such chemically modified RNA is more costly and complicated than letting bacteria do it, the company says. The technology was developed in the lab of Chiang Li at Beth Israel Deaconess Medical Center, from which Cequent now licenses the technology.

The company’s first target gene is catenin beta-1, which, when overly active, causes familial adenomatous polyposis, a condition that nearly always leads to colon cancer. In a 2006 Nature Biotechnology paper, Li and colleagues demonstrated that when mice swallow the engineered bacteria, the bacteria travel through the gastrointestinal tract, enter the cells lining the gut, and die. The shRNA remains and switches off the catenin beta-1 gene in the intestinal cells. Based on these results and continuing studies, the company hopes to begin testing its first drug in humans in 2008.

“What we do is fairly different from what other people do,” says Johannes Fruehauf, director of preclinical and clinical development at Cequent. Most other RNAi companies synthesize short interfering RNA (siRNA)—another RNAi mediator—from scratch. “We take the biologic approach.”

Door-to-door delivery

Many companies are vying to be first to get an RNAi-based drug approved, and several of them already have siRNAs in early clinical trials. These trials, though, are testing siRNAs for organs, like the lungs and eyes, that can easily take up unmodified siRNAs without the need for drug delivery systems. For example, Cambridge-based Alnylam Pharmaceuticals has developed an inhaled version of siRNA to treat a lung disease called respiratory syncytial virus; lung cells can be penetrated by unmodified siRNAs. But for most other tissue and organs, such as the intestinal tract, RNAi drug developers are working on delivery systems to get their RNA molecules into the target cells.

“If RNAi therapeutics fulfill the promise in the future, we will see various ways of delivery for various organs,” Fruehauf says.

Cequent’s bacterial carriers can theoretically be used to silence genes anywhere there’s a cell lining that can be colonized by bacteria—the gut, genital tract, bladder. So the company is also developing treatments for inflammatory bowel disease and human papillomavirus.

Watch the messenger

Some researchers are concerned that Cequent’s bacteria will trigger immune responses in humans, which could destroy the carriers before they get a chance to deliver their cargo. But Fruehauf says they have taken pains to avoid this.

His team looked to see whether genes involved in the immune response were turned on in cells when given the bacterial treatment. They weren’t, but Fruehauf admits that he doesn’t know yet what will happen in humans.

Fruehauf adds that the E.coli that Cequent uses is harmless to humans; the bacteria are engineered to not be able to grow and multiply in the body.