Development and validation of diagnostic biomarkers for B-cell lymphoma using EpiSwitch (TM) profiling of whole blood: From humans to canines

Abstract Backgound: Changes in chromosome conformation are strongly associated with different clinical phenotypes and outcomes for a variety of diseases. Here, we used the EpiSwitchTM platform technology to evaluate chromosome conformation signatures (CCS) as biomarkers for detection of canine diffuse large B-cell lymphoma (DLBCL). We examined whether established, systemic liquid biopsy biomarkers previously characterized in human DLBCL patients by EpiSwitchTM would translate to dogs with the homologous disease. Orthologous sequence conversion of CCS from humans to dogs was first verified and validated in control and lymphoma canine cohorts. Methods: Blood samples from dogs with DLBCL and from apparently healthy dogs were obtained as part of the comparative cancer genomics and veterinary clinical trials programs of the Animal Cancer Care and Research Program of the University of Minnesota. Dog owners provided signed informed consent, and all studies were done under protocols approved by the Institutional Animal Care Committee of the University of Minnesota. All of the dogs diagnosed with DLBCL were part of the LICKing Lymphoma trial. Blood samples were obtained from each dog prior to initiating treatment at day+5 after the experimental intervention, but prior to initiating doxorubicin chemotherapy. EpiSwitchTM technology (Oxford Biodynamics) was used to monitor systemic epigenetic biomarkers for CCS. This application was based on published methodology for validated predictive biomarkers for response to treatment, systemic blood-based monitoring of oncologic conditions, and proprietary programs in collaboration with Roche/Genentech for liquid biopsy development for DLBCL prognosis. Results: A 11-marker classifier was generated with whole blood from 28 dogs, 14 diagnosed with DLBCL and 14 controls with no apparent disease, from a pool of 75 EpiSwitchTM CCSs identified in human DLBCL. Validation of the developed diagnostic markers was performed on a second cohort of 10 dogs: 5 with DLBCL and 5 controls. The classifier delivered stratifications for DLBCL vs. non-DLBCL with 80% accuracy, 80% sensitivity, 80% specificity, 80% positive predictive value (PPV), and 80% negative predictive value (NPV) on the second cohort. Conclusions: The established EpiSwitchTM classifier contains strong systemic binary markers of epigenetic deregulation with features normally attributed to genetic markers: the binary status of these classifying markers is statistically significant for diagnosis, and it is translatable across species. The data suggest that certain features of the higher-order structural chromatin organization associated with DLBCL, and perhaps other homologous cancers, may be evolutionarily conserved. Altogether, these findings highlight the potential of the EpiSwitchTM approach for disease diagnosis and further applications using liquid biopsies in humans and dogs. Citation Format: Lauren J. Mills, Ewan Hunter, Aaron L. Sarver, Davis Seelig, Jennifer Back, Louis James, Navin Jandor, Polina Brayer, Thomas Lavin, Ryan Powell, Matthew Salter, Jayne Green, Aroul Ramadass, Alexandre Akoulitchev, Jaime F. Modiano. Development and validation of diagnostic biomarkers for B-cell lymphoma using EpiSwitchTM profiling of whole blood: From humans to canines [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr A42.