Leap Therapeutics and Flagship Bioscience have developed an image analysis RNAscope assay that is being used for prospective patient enrollment in a clinical trial. The companies believe this is the first example of an RNAscope assay using a digital image analysis solution for patient enrollment. They describe how to the technology is being used to identify patients likely to benefit from Leap’s DKN-01, its anti-Dickkopf-1 (DKK1) antibody. The article is featured in Nature Scientific Reports.
“Our technology, combined with our scientific process and pathology oversight allows you to quickly find the right patients and get to your endpoints more rapidly,” said Trevor Johnson, CEO of Flagship Biosciences, which specializes in tissue imaging. “Image analysis also provides a superior return on investment by saving time and helping get drugs to market more quickly. Our ability to take a completely novel pathology approach and turn it into a CLIA-validated diagnostic test to help our clients is extremely gratifying.”
RNAscope is an in situ hybridization technique optimized on multiple autostainer platforms. It is increasingly used in research and clinical studies. The scope’s probes are designed to selectively target RNA and overcome sensitivity and specificity limitations of antibodies used for immunohistochemistry. It is “exquisitely sensitive,” the researchers write, can detect partially degraded RNA, and the signal amplification chemistry allows for detection of a single RNA molecule per cell. Staining appears as one dot per RNA in the cell, and this allows manual semi-quantification or digital approaches. This method is believed to provide improved precision, accuracy, and lack of bias from manual scoring.
In this report, Leap and Flagship’s work centered on the development and validation of a DKK1 RNAscope chromogenic in situ hybridization (CISH) assay and digital image analysis solution. DKK1 is a secreted modulator of Wnt signaling that is frequently overexpressed in tumors and associated with a poor prognosis for patients. DKN-01 is a humanized monoclonal therapeutic antibody that binds to and blocks the activity of DKK1 and has demonstrated clinical activity in gastric/gastroesophageal junction (G/GEJ) adenocarcinoma patients with elevated tumoral expression of DKK1 RNA.
Leap and Flagship have validated the DKK1 RNAscope assay and accompanying digital image analysis solution as specific, sensitive, accurate, and reproducible according to Clinical Laboratory Improvement Amendments (CLIA) guidelines, and their work is currently being applied to prospectively identify G/GEJ patients with elevated tumoral expression of DKK1 for treatment with a DKN-01 plus tislelizumab combination. Additionally, the companies are using the DKK1 RNAscope assay and digital image analysis solution for a retrospective analysis of G/GEJ patients treated with DKN-01 in combination with tislelizumab and chemotherapy.
Because of the challenges in manual semi-quantification of RNAscope tissue staining, Leap and Flagship developed a novel digital image analysis algorithm that identifies tumor cells and quantifies DKK1 signal.
“A potential challenge with RNAscope is manual scoring, which requires a pathologist to score the tissue at a high magnification to visualize and count the number of stained dots that appear in tumor cells,” said Michael Kagey, PhD, Senior Director of Translational Medicine at Leap Therapeutics. “Since this can lead to slow, inaccurate, and non-reproducible scoring, we worked with Flagship to develop a digital algorithm. The digital algorithm reduces pathologist time, potential variability from manual scoring and allows us to reliably screen for patients who may benefit from our therapy.”
In addition to the prospective screening of patients, the work is also further advancing the companion diagnostic development of the RNAscope assay and could generally be used as a guide for the validation of RNAscope CISH assays with digital image quantification.
“Our clinical development has been enhanced by the rapid, prospective patient screening that has happened as a result of using the DKK1 RNAscope CISH assay and digital image analysis solution,” said Douglas E. Onsi, President and CEO of Leap Therapeutics. “As a result of the partnership between Leap and Flagship, the patients who we believe will best benefit from our drug are now being included in our trial. We look forward to further collaborating with Flagship Biosciences.”
Leap Therapeutics is developing targeted and immuno-oncology therapeutics. DKN-01 is in clinical trials in patients with esophagogastric, hepatobiliary, gynecologic, and prostate cancers.