A novel PAThway based RNA and DNA Integration with Tumor Organoid Testing (PATRIOTTM) platform predicts therapeutic options in cohorts with MET overexpression and CDKN2A downregulation in patients with colon and pancreatic cancers

Abstract Background: Cancer therapy has witnessed great progress over the last 50 years with advancements in diagnostic tools to enable more precise treatment. With the development of next-generation sequencing, the field of precision oncology has been expanded to tailor treatments to a patient's mutational profile, however, there is a need for additional information such as RNA Differential Expression (DE) to match more patients to potentially beneficial drugs. We have previously described our PATRIOT platform, which integrates RNA DE analysis, NGS, and high throughput patient-derived organoid models to identify new therapeutic targets. In our previous study, we tested the PATRIOT platform on a patient with predicted KRAS and IDHI inactivation resulting in inhibition of DNA damage repair pathway. Patient-derived tumor organoids showed a significant response to the suggested treatment, Olaparib, supporting the reliability of PATRIOT prediction. To further validate this platform, we interrogated the predictive efficacy of PATRIOT in cohorts of patients characterized by CDKN2A downregulation or MET overexpression. Methods: Following PATRIOT analysis, patients with predicted CDKN2A downregulation or MET overexpression consisting primarily of colon and pancreatic cancer were grouped into two cohorts. Patient-derived tumor organoids were tested for sensitivity to drugs matched to the predicted targets as single agent or in combination, using a 4-fold dilution followed by 72h viability assay. Drug cytotoxicity and Bliss Synergy were analyzed using GraphPad Prism and Combenefit. All screenings were subjected to stringent quality control measures and normalized against untreated organoids. Results: Our analysis identified patients characterized by MET overexpression suggesting crizotinib, a small-molecule tyrosine kinase inhibitor of the c-MET receptor, as sequencing-matched therapy. Tumor organoids showed sensitivity to crizotinib (IC50 5.74 M+/- 3.2), validating our initial predictions. In a separate cohort, tumor organoids generated from patients characterized by downregulation of CDKN2A were treated with Palbociclib, a CDK4/6 inhibitor. Tumor organoids showed limited response to treatment (IC50 57.75 M+/- 25.1), which has been reported in an earlier clinical trial (NCT01740427). However, recent studies have shown that Pablociclib treatment enhances cisplatin cytotoxic effect in several solid tumor models through the CDK4/6-cyclin D1-RB-E2F pathway (NCT02897375). When tumor organoids were co-treated with Palbociclib and Cisplatin, significant synergy was observed (moderate-strong). In summary, PATRIOT analysis provided bioinformatic predictions of pathway based therapeutic options that were validated using tumor organoid platforms. Citation Format: Anna Larson, Taylor Bargenquast, Sara Byron, Anish Raju, Avijit Podder, Shelby Rheinschmidt, Tithi Ghosh Halder, Samuel Sampson, Sydney Adamson, Serina Ng, Kate Gutowsky, Alexis Weston, Trason Thode, Justin Moser, Erkut Borazanci, Mohan Kaadige, Nicholas Schork, Raffaella Soldi, Sunil Sharma. A novel PAThway based RNA and DNA Integration with Tumor Organoid Testing (PATRIOTTM) platform predicts therapeutic options in cohorts with MET overexpression and CDKN2A downregulation in patients with colon and pancreatic cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1069.