Getting closer

USC researchers have moved one step closer to understanding how the body fights harmful antigens – foreign molecules that trigger an immune response.

The team successfully simulated a mutation process that diversifies the proteins, or antibodies, responsible for immunity – a phenomenon known as somatic hypermutation. This process enables the body to fight off a wide range of diseases.

Their findings are detailed in the July 3 issue of the journal Nature.

“When performing laboratory – or in vitro experiments – you always hope to get results that are close to the real thing,” said John Petruska, one of the paper’s authors and a professor of molecular biology in USC’s College of Letters, Arts & Sciences. “In this case, it is fascinating to discover that the somatic hypermutation process in vitro is nearly identical to that in a natural environment.”

“This is the first step in building an in vitro system that would completely mimic the body’s immune response,” Petruska added.

One of the first tactics the immune system uses to fight off foreign molecules is the production of protective antibody proteins, which are unique in their unlimited ability to diversify.

As one’s immune response intensifies, antibodies undergo mutations that enable them to attack foreign molecules more forcefully, said Phuong Pham, the paper’s lead author and a USC molecular biology postdoctoral researcher.

That process is known as somatic hypermutation.

Those more powerful antibodies allow the immune system to respond quickly and effectively to pathogens, particularly those from previous infections. In other words, the antibodies are much like soldiers sent to fight an enemy they’ve encountered in the past.

People whose immune systems lack the ability to create these strengthened antibodies may suffer from recurring bacterial and viral infections and do not respond to vaccinations.

Somatic hypermutation requires an enzyme called AID (Activation-Induced Cytidine Deaminase) which works on single-stranded DNA – a discovery made by the USC team earlier this year.

By allowing AID to work on single-stranded viral DNA containing a mutational marker gene, the researchers (using specialized laboratory techniques) were able to identify which DNAs contained mutations and which did not.

“The action of AID yielded the same specific mutational hot and cold spots along DNA strands that are observed in human antibody proteins,” explained Myron F. Goodman, a professor of molecular biology and chemistry in USC’s College of Letters, Arts & Sciences and senior author of the Nature paper.

Those “hot” spots, identified by specific DNA sequences, allowed the researchers to clearly see where the mutations took place. In fact, the experiment yielded 14 out of 15 hot spots with perfect DNA sequences, demonstrating that the mutation process had gone off without a glitch.

“Remarkably, the results showed that AID acting alone on single-stranded DNA simulated the highly complex somatic hypermutation process that occurs in humans,” Goodman said.

Furthermore, the team’s data revealed that the AID enzyme works its way along individual DNA strands, as opposed to jumping from one strand to another.

Because many of the DNA strands remained untouched as part of this methodical process, the team found that 98 percent of its experimental DNA had no mutations.

Among the 2 percent that did, half exhibited between one and 20 mutations, while the other half showed up to 80.

“It confirms that AID is working on individual pieces of DNA, instead of jumping around,” Goodman said.

Overall, the USC team of researchers was impressed by AID’s role in the entire process.

“AID can’t account for somatic hypermutation by itself because we know that other enzymes are involved,” Goodman explained. “But it’s pretty darn impressive to see that AID accounts for almost everything in the mutational targeting process.”

The team’s work is yet another feat in the quest to uncover how the body’s immune system fights an enormous array of antigens, employing a delicate balance of mutations.

“Mutations can be both helpful and harmful,” Petruska said. “Balance is key.”