Researchers from the Wistar Institute are using a $1 million grant from Pennsylvania's Commonwealth Universal Research Enhancement Program to develop a gene expression-based blood test to detect early-stage lung cancer.
The researchers, led by Louise Showe, identified a 29-gene signature in a 267-patient study that used Illumina microarrays to measure gene expression levels in peripheral blood mononuclear cells. That signature, described in a paper published last August in Clinical Cancer Research, predicted the presence of lung cancer with 86 percent accuracy, the Wistar researchers reported.
Armed with the CURE funding, Showe and colleagues are now planning to evaluate 600 samples in order to validate the signature and improve its accuracy to 90 percent or greater. In addition, they also plan to simplify the sample-collection workflow and evaluate Qiagen's PAXgene blood-collection tubes for this purpose.
As part of the two-year project they will also explore whether to move the gene signature to a PCR platform or keep it on an array for final clinical development.
Showe, a professor in Wistar's Molecular and Cellular Oncogenesis program who also serves as associate director of the institute's Center for Systems and Computational Biology, told BioArray News via e-mail that the researchers used microarrays to identify candidate markers and will now "test this panel on a variety of platforms, most PCR-based, to find the most sensitive and reliable platform for clinical applications."
She noted that her group previously moved a biomarker panel for cutaneous T-cell lymphoma from an array platform to PCR — work described in Blood in 2006.
"There are many more platforms available for transitioning from arrays in 2012 and we have been exploring options," she said.
Aiding CT Scanning
The Wistar team is developing the test in order to help clinicians determine whether suspicious lung nodules identified by computerized tomography scan are malignant — information that could reduce unnecessary surgery or biopsies.
While CT screening has been shown to reduce mortality from lung cancer by detecting it earlier, it has a high false-positive rate. For example, a study published last year in the New England Journal of Medicine by the National Cancer Institute's National Lung Screening Trial found that of nearly 27,000 patients who underwent CT scanning, more than 90 percent of the nodules detected were benign.
"Classification of suspicious nodules is a real dilemma in the lung cancer field," Showe said. Her team and a number of other groups are turning to blood-based approaches in hopes of complementing these CT results with molecular classification of nodules as benign or malignant.
A number of groups are looking at protein signatures as opposed to gene expression signatures for this indication. For example, researchers from the University of Pittsburgh published a study earlier this year in the Journal of Thoracic Oncology describing a panel of ten serum protein markers that distinguished between malignant and benign lung nodules in a group of 30 cases and 30 controls with accuracies of 83.3 percent and 89.2 percent for Stage I and II lung cancers, respectively.
In addition, several companies — including Integrated Diagnostics, Quest Diagnostics' Celera, and SomaLogic — are looking to commercialize protein-based tests for early cancer detection.
Showe said it's likely that the gene expression-based approach and the protein-based tests could be "synergistic." Her group is also evaluating the use of miRNA expression alongside gene expression with the aim of developing a "multi-analyte platform," she said.
One potential advantage of the Wistar team's assay, Showe said, "is the ease of sample collection and sample stabilization of the whole-blood sample, which would facilitate collection in a physician's office."
The sample collection step is crucial to the clinical development of the assay and is a key part of the CURE-funded project, Showe noted.
"In developing a clinical test, standardizing sample collection is the most important step," she said. "Our published study was carried out with samples collected under conditions we had outlined from the beginning. We learned early on that although each collection site tries to collect and process samples in a standard way, when there are many steps involved the variability from site to site increases. We have tried to eliminate that burden from the clinical sites in the present study by simplifying that critical process."
The Wistar researchers believe that Qiagen's PAXgene blood-collection tubes will help them meet this goal. In their abstract for the CURE grant, they note that the tubes "provide rapid stabilization of RNA in whole blood at the moment of the blood draw so that a reproducible and highly standardized blood collection system can be established."
They add that their preliminary results from microarray studies on 48 cancer and control samples in PAXgene "support the viability of this approach and further support the feasibility of moving our [peripheral blood] results to a commercially viable platform."
The sample-collection step will also be key to the eventual commercialization of the test. Showe said that the Wistar team has discussed commercialization of the assay with "several companies" based on the preliminary results, but "it was felt that we needed the PAXgene results first."