• Optimal therapeutic targeting of cancer involves clonal signals which are expressed within all cancer cells
• Gradalis applies a novel clinically relevant approach to determine clonal tumor mutation burden/neoantigens, thereby potentially expanding the use of immunotherapies to enable more consistent and effective clinical response and optimally target cancers
• Analysis shows cTMB signal identified in patients’ tumor tissue is preserved in Gradalis’ Vigil® investigational therapy

Gradalis, Inc., a clinical-stage biotechnology company focused on personalized anti-cancer therapy for patients with ovarian and other cancers, announced a peer-reviewed publication in Scientific Reports. The paper details the methods and validation of Gradalis’ exome sequencing procedure and associated bioinformatics pipeline for identifying signal patterns that drive cancer growth and spread. Titled “Exome sequencing shows same pattern of clonal tumor mutational burden, intratumor heterogenicity and clonal neoantigen between autologous tumor and Vigil product”, the publication provides insight into the science and implications of this key discovery. The study highlights a novel approach to identify clonal mutation signals which provide the greatest potential to result in clinical benefit to immunotherapy as well as the optimal cancers amenable to this therapeutic approach. Furthermore, the research offers a deeper mechanistic insight into the effects observed with Gradalis’ Vigil, an investigational immunotherapy platform being developed for various cancers. The full text of the article can be found here.

“Clonal signals, specifically levels of clonal tumor mutation burden and clonal neoantigens, define the genetic signals which go awry in normal cells, forcing them to take on cancer characteristics. Clonal signals are maintained as cancer cells grow, and we believe this is the optimal molecular target to identify and therapeutically attack in the fight against cancer,” stated John Nemunaitis, M.D., Gradalis’ Chief Scientific Officer. “Published retrospective data demonstrated that patient response to immunotherapy, as measured by overall survival advantage, is correlated with high clonal tumor mutation burden, high clonal neoantigens, and/or low intratumor heterogeneity. We believe that our proprietary exome sequencing approach will play a key role in identifying those cancers most likely to respond to gemogenovatucel-T and potentially enable the better targeting of other immunotherapies.”

Normal immune system function identifies cancer cells for destruction through dendritic-T cell interaction. This interaction is most effective when involving signals present on all cancer cells (clonal signals) rather than limited subsets of cancer cells (subclonal signals). The Scientific Reports publication describes the development of a clinically applicable method for determination of clonal Tumor Mutation Burden (cTMB), clonal Neoantigens (cNEO), and Intratumoral Heterogeneity (ITH) using matched tumor biopsy and peripheral blood mononuclear cell samples. Gradalis engaged Frontage Laboratories (Deerfield Beach, FL) to construct the bioinformatics pipeline and conduct the analysis. Previously published exome sequencing data sets from an immunotherapy clinical trial and clonal deconvolution validation study were used to verify the performance of the developed bioinformatics pipeline. The wet lab exome sequencing and bioinformatic process steps were further qualified by analyzing samples of Vigil, Gradalis’ engineered autologous tumor-based therapy, and the original tumors used to construct Vigil from a set of patients.

Levels of cTMB, cNEO, and ITH determined for Vigil and the original tumor were strongly correlated to each other across a set of patients, demonstrating the reliability of the assay. This research also shows that construction of Vigil did not negatively impact the clonal signal.

“The developed exome sequencing platform and bioinformatic pipeline utilized the best available exome sequencing technology and open-source software algorithms to create a high throughput system for measurement of cTMB, cNEO, and ITH levels. We expect that this approach will be applicable to identification of patients likely to respond to immunotherapy across multiple types of cancer,” said lead author, David Willoughby, Ph.D