Gradalis Announces Development of Clinically Relevant Exome Sequencing Bioinformatics Pipeline to Determine Clonal Tumor Mutation Burden

• 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
  

/EIN News/ -- DALLAS, March 14, 2025 (GLOBE NEWSWIRE) --   

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.

For additional information, visit gradalisinc.com or contact Mark Early, General Counsel and Director Investor Relations, at
Mark Early
214.442.8161
mearly@gradalisinc.com

About Exome Sequencing Procedure and Associated Bioinformatics Pipeline
Paired tumor and normal (typically PBMC) samples are used to prepare DNA libraries containing exome sequences tagged with unique molecular identifiers (UMI) which are sequenced on Illumina sequencers to a high coverage depth (930x tumor, 130x normal). Raw sequence reads are then processed into optimized binary alignment map (BAM) files using the UMI information. These BAM files are inputted into bioinformatic modules for annotating single nucleotide variants and small insertions and deletions, for determination of allelic copy number and for calling MHC-1 alleles. The output data from these modules is then used to predict the sequences of peptide neoantigens and to perform clonality analysis in order to assign each SNV and InDel in a patient tumor sample to a primary clone or subclone. A final summary report provides the cTMB, cNEO, and ITH levels for each patient. A detailed variant level-report is also produced which contains information about the clonality of each identified non-synonymous sequence variant along with the sequence of its associated neoantigen peptide and its expected affinity of binding for the patients MHC-1 complex.

About Vigil
Vigil® is a novel, triple function immunotherapy platform that modifies a patient’s tumor by using bi-shRNA to reduce furin, an enzyme which facilitates immunosuppressive TGF beta protein production, and to maximize DNA expression of GM-CSF, which stimulates the immune system and attracts key immune system effector cells, including T-cells. By utilizing the patient's own tumor as the antigen source, Vigil is designed to elicit an immune response that is specifically targeted and broadly relevant to each patient's unique clonal tumor neoantigens. In patients with HRP ovarian cancer and high cTMB, where there is a high unmet medical need, Vigil has been designated a Regenerative Medicine Advanced Therapy (RMAT) by the FDA on the basis of a statistically significant and clinically meaningful improvement in OS.

Additionally, Phase 1 results in an “all-comer” clinical trial showed positive signals of activity in 19 different tumor types and some patients treated with Vigil remained in the study 48 months later. Vigil has also demonstrated safety and benefit in two separate pilot studies when administered concurrently or in sequence prior to treatment with check point inhibitor therapy. The sequential treatment results support the hypothesis that Vigil administration prior to starting checkpoint inhibitor therapy may focus the immune effector population to the cancer, potentially enhancing activity and limiting off target side effects.

Vigil is the first cellular immunotherapy to demonstrate longer-term survival benefits in a randomized controlled trial of patients with solid tumors. The results of the company’s Phase 2b study have been published in Lancet Oncology, Gynecologic Oncology and presented at the American Society of Clinical Oncology.

About Gradalis, Inc.
Founded in 2006, Gradalis is a privately held, clinical-stage biotechnology company developing a new category of personalized therapies based on proprietary bi-shRNAi technology. Its lead product, called Vigil, is an immunotherapy that has been tested in multiple studies in ovarian and other cancer tumor types. In patients with HRP ovarian cancer and high cTMB, where there is a high unmet medical need, Vigil has been designated a Regenerative Medicine Advanced Therapy (RMAT) by the FDA on the basis on a statistically significant and clinically meaningful improvement in OS.

Gradalis’ Vigil platform uses the patient’s immune system to target the entire tumor. Based on multiple clinical studies, Gradalis has developed a pioneering oncology platform that is designed to decloak the patient’s tumor clonal neoantigens, reactivate the immune system, and summon key effector cells to deliver a durable clinical response. When combined, these are a powerful Trifecta of anti-cancer activities, potentially eliminating even the elusive metastatic cells, as shown in Phase 2 clinical studies in ovarian cancer. Our clinical trials have also demonstrated that Gradalis’ platform is better tolerated compared to standard cancer treatments since Vigil uses the patient’s immune system operating within its natural state of balance rather than in an artificial overdrive as with some technologies. Vigil utilizes proprietary bi-shRNA technology that has been proven to silence multiple genes EWS/FLI1, KRAS, STMN1, PDX-1 in a variety of cancers and has the potential to be used in other diseases. To learn more, visit www.gradalisinc.com

Forward-Looking Statements

This press release contains forward-looking statements, including, without limitation, statements regarding the success, cost, and timing of our product development activities and clinical trials, our plans to research, develop, and commercialize our product candidates, and our plans to submit regulatory filings and obtain regulatory approval of our product candidates. These forward-looking statements are based on Gradalis’ current expectations and assumptions. Because forward-looking statements relate to the future, they are subject to inherent uncertainties, risks, and changes in circumstances that may differ materially from those contemplated by the forward-looking statements, which are neither statements of historical fact nor guarantees or assurances of future performance. Important factors that could cause actual results to differ materially from those in the forward-looking statements include but are not limited to: (a) the timing, costs, and outcomes of our clinical trials and preclinical studies, (b) the timing and likelihood of regulatory filings and approvals for our product candidates, and (c) the potential market size for our product candidates. These forward-looking statements speak only as of the date made and, other than as required by law, we undertake no obligation to publicly update or revise any forward-looking statements. This press release does not constitute an offer to sell, or a solicitation of an offer to buy, any securities.