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March 26, 2003

New proteomic techniques reveal workings of bacteria linked to cystic fibrosis

Researchers have identified a cell signaling system that may help the bacterium Pseudomonas aeruginosa establish itself in the lungs of cystic fibrosis patients. The researchers used a new technology to seek insights into an important and elusive enemy, and say the findings are important for biology and potentially important for therapy.

The researchers identified the activation of this signaling system by the use of new quantitative proteomic technology that analyzed Pseudomonas samples from the lungs of children with cystic fibrosis. Proteomics is the method for analyzing and cataloguing a complete cellular complement of proteins, which are produced based on information encoded by genes and are the workhorses of all living cells.

The analysis by researchers at University of Washington and the Institute for Systems Biology indicated that quorum sensing — bacterial communication using small molecular signals — may help P. aeruginosa become virulent. P. aeruginosa is so virulent that it will often kill cystic fibrosis patients. The highly sensitive quantitative proteomic analysis of a whole bacteria performed in this study implicates a cell signaling system, Pseudomonas quinolone signal, or PQS, that may help the bacteria adapt within the cystic fibrosis patient’s airway and defy the body’s efforts to suppress it.

The findings were published in the March 4, 2003, issue of the Proceedings of the National Academy of Sciences.

“It appears that PQS production is increased in isolates from young children with cystic fibrosis, as opposed to the production by laboratory strains of Pseudomonas,” says Dr. Tina Guina, research assistant professor in the UW Department of Pediatrics. “The children’s lungs are colonized with Pseudomonas very early in life, as a result of an unknown innate immune defect associated with mutation of a chloride channel. Further studies may show whether PQS might be important for early adaptation to the airways of young cystic fibrosis patients. If it is, then perhaps someday we can interfere with PQS production and help cystic fibrosis patients.”

Pseudomonas aeruginosa is an environmental bacterium that is found almost anywhere — dirt, water, and you name it. The bacterium has a remarkable capacity to adapt to different environments and live even when nutrients are very limited. It does not colonize the lungs of healthy individuals. But lungs of people with cystic fibrosis get colonized early in life. Almost all CF patients are infected with P. aeruginosa by the teenage years and approximately half are colonized by 3 years old. The bacterium will remain in cystic fibrosis patients for decades, causing troublesome and eventually fatal inflammation. Pseudomonas is the most common source of chronic and fatal lung infections for those with CF, and also poses danger to burn and cancer patients, persons on respirators or those requiring catheters.

Based on previous analysis of children ages 3 and younger, researchers suspected that changes within P. aeruginosa early in the child’s life allow the bacteria to work up such tough defenses. So researchers would like to find areas of vulnerability in P. aeruginosa as early in life as possible, since recent studies indicate that early intervention with antibiotics can possibly eradicate the bacteria. The UW research team analyzed samples of Pseudomonas aeruginosa from the airways of children ages 6 to 36 months, the first time samples have been so thoroughly analyzed among patients so young. These samples were collected by UW pediatrics faculty Drs. Bonnie Ramsey and Jane Burns at Children’s Hospital and Regional Medical Center in Seattle. Almost 10 years ago, these clinical CF researchers had the foresight to collect these samples in hopes of understanding more about CF airway disease.

The research utilized quantitative proteomic analysis using mass spectrometry pioneered by Dr. Ruedi Aebersold’s research group when he was at the UW in Genome Sciences and Mike Gelb in UW Chemistry. The technology was further developed after Aebersold’s move to the Institute for Systems Biology and was applied in this study to identify quantitative changes in protein expression in P. aeruginosa.

“This is one of the first proteomic studies of the protein content of an entire organism,” Guina says.

“We are excited that one of the first applications of the technology we developed to a clinically important problem has yielded new insights that may ultimately help patients,” Aebersold said.

Using the new technology, more than 1,000 proteins were surveyed. Computer analysis of the data suggested new ways P. aeruginosa uses to adapt to the conditions it encounters in airways. This information was then used to analyze patient samples to determine that PQS is activated in bacteria from CF airways.

“This could well be part of the method that Pseudomonas uses to keep itself alive in the lung, before it transforms its genome and mutates into a killer,” Guina says. In some cases, PQS production diminishes in samples from patients who are older than 3.
“It may be that PQS has already done its damage by the time the patient reaches 36 months, and other processes continue to help Pseudomonas thrive in the airway.”

These ongoing studies of P. aeruginosa are part of the comprehensive UW Cystic Fibrosis Research and Development Program, which is directed by Dr. Samuel Miller, senior author of the paper and a UW professor of medicine. Among other activities, researchers are studying the diversity of P. aeruginosa in the airway of cystic fibrosis patients in order to better understand the pathogenesis of pulmonary infection. Miller is also involved in the Keck Center for Microbial Pathogenesis, which is seeking to develop drugs for P. aeruginosa infection in cystic fibrosis.

Other authors of the paper include Aebersold and Drs. David R. Goodlett, Jimmy Eng, Samuel Purvine and Eugene C. Yi of the Institute for Systems Biology in Seattle.

The UW School of Medicine is part of UW Medicine, which also includes UW Medical Center, Harborview Medical Center, UW Physicians, UW Physicians Neighborhood Clinics, and the UW’s membership in the Seattle Cancer Care Alliance and the Children’s University Medical Group. UW Medicine has major academic and service affiliations with the Children’s Hospital and Regional Medical Center, the Fred Hutchinson Cancer Research Center, and the Veteran’s Administration Medical Centers in Seattle and Boise. The School of Medicine is consistently among the top five recipients of federal funding for biomedical research; its 1,600 regular faculty include four Nobel Laureates, 25 members of the National Academy of Sciences, and 26 members of the Institute of Medicine.

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