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Researchers Develop GeneChip Approach for Detecting Pneumonia in Critically Ill

NEW YORK (GenomeWeb News) – Pneumonia can be difficult to identify in some hospitalized patients due to health complications that interfere with typical diagnostic tests. Now, scientists have translated gene expression studies in mice into a potential method for detecting pneumonia in critically ill, ventilated patients using Affymetrix’s GeneChip technology.
Researchers from Washington University in St. Louis identified hundreds of genes in mice whose expression specifically changes when they are infected with pneumonia-causing bacteria. They found similar gene expression changes in the infection-fighting leukocytes, or white blood cells, of ventilated patients who developed pneumonia. The research, published in the journal PLoS ONE online this week, suggests microarray expression profiles can both identify pneumonia in such patients — leading to more rapid treatment — and track patient recovery.
“[I]nfectious complications are not only common in intensive care units but also difficult to diagnose. This has contributed to inappropriate use of broad-spectrum antibiotics and the emergence of multi-drug resistant organisms,” the authors wrote.
Normally, the respiratory system filters air as it enters the lungs. But when patients are on ventilators, they have a breathing tube inserted directly into their lungs, bypassing this filter. Because the air these patients receive is humidified, it is more likely to become contaminated by pathogenic microorganisms. Consequently, up to a third of ventilated patients develop pneumonia, according to a statement from Washington University.
Since conventional tests for pneumonia rely on markers of infection that may be present in the hospitalized patients even before they develop pneumonia, the condition may be missed or misdiagnosed. For this study, senior author Perren Cobb, a surgeon and geneticist at Washington University in St. Louis, and his colleagues attempted to identify more specific markers for immune activation caused by pneumonia.
First, they did gene expression studies in mice that were injected with the pneumonia-causing bacteria Pseudomonas aeruginosa or Streptococcus pneumoniae. To determine the effects of inflammation that was independent of actual pneumonia, they also injected some mice with the P. aeruginosa endotoxin alone.
Using Affymetrix GeneChip microarray analyses, they identified 219 genes that were differentially expressed in conjunction with pneumonia as opposed to more general, widespread inflammation.
In an effort to translate this research into a clinical setting, the team then looked for similar gene expression changes in intensive care patients, focusing on 11 who developed pneumonia within more than two days of going on a ventilator. The team drew blood from these patients every 48 hours, hybridizing white blood cell cRNA against Affymetrix’s HG-FOCUS array.
After assessing the expression of more than 8,000 genes, they found 85 whose activity changed in the patients who subsequently developed pneumonia — many of them coding for proteins involved in immune system activation.
The team also confirmed the diagnostic potential of the chip approach in a smaller group of patients. Interestingly, the researchers reported, they were able to track illness and recovery using so called riboleukograms of white blood cell gene expression markers.
“This is an important step toward the development of a specific molecular test for diagnosing infection — in particular pneumonia — and predicting patients’ recovery,” Cobb said in a statement. “If we could determine which patients are destined to develop pneumonia based on early changes in the activity of genes that regulate immune response, we could give them antibiotics sooner, with the hope that we might be able to prevent or curtail the infection.”

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